Spicer assumed he would be on the list, the official said, adding that meeting the Pope was one of the bucket list items Spicer, a Catholic, wanted to check off during his tenure as press secretary.
The presidential snub raised fresh questions Thursday about Spicer's standing as the chief White House spokesman.
The meeting here at Vatican City placed the ever-shifting pecking order of a tumultuous White House on full display.
Standing alongside the President as he met the Pope inside the Sala del Tronetto here were his wife, Melania, dramatically veiled in lace. To her right, eldest daughter, Ivanka, and her husband, Jared, each senior Trump advisers and near-constant presences in Trump's close circle. Secretary of State Rex Tillerson and national security adviser H.R. McMaster -- Trump's highest-ranking foreign policy aides -- stood flanking Francis.
Those were the expected faces. But there were others there, too -- less familiar yet nonetheless critical to the West Wing ecosystem. Hope Hicks, Trump's communications adviser; Keith Schiller, his former bodyguard; and Dan Scavino, his social media master, all stood solemnly as Trump greeted the Pontiff.
On a foreign trip told primarily in images, the staff dynamics of Trump's White House have been on full view, from the lavish welcome in Saudi Arabia to the exclusive audience Wednesday with Pope Francis.
Also absent from the Vatican visit: Kellyanne Conway, the senior counselor who remained behind in Washington; Reince Priebus, the chief-of-staff who dropped off Trump's trip after the first stop; and Steve Bannon, the fire-throwing chief strategist who, as the boss of Breitbart, oversaw articles harshly critical of the Pope.
The photographs at the Vatican on Wednesday underscored a point that often goes unspoken in the Trump White House: old friends and family reign above all. Staff is just that -- staff.
Ultimately, the formalities of West Wing titles mean less than family ties or longevity in Trump world. Spicer, for example, is an assistant to the President -- the top-ranking title for White House aides -- and Catholic, but was informed before the meeting there wasn't room for him on the roster.
Spicer did not respond to a request for comment.
Asked about Spicer not being included in the group that met the Pope, a source close to the White House said: "Wow. That's all he wanted," adding it should "very much" be seen as a slight.
Schiller, meanwhile, is a deputy assistant to the President -- a lower rank than Spicer -- but he is an aide with few equals, a body man who rarely is away from the President, whether he's on the golf course or the Sistine Chapel.
And Ivanka Trump and Jared Kusher -- who are both Jewish but nonetheless attended the Vatican session with the President -- have rarely been away from the President's side as he navigates the tricky international politics of the Middle East and Europe.
"It was a very small delegation that joined the President," a White House official told CNN.
Two additional senior White House officials said the Vatican was very "strict" on the number of people who would be allowed to join the talks.
But previous administration officials who helped orchestrate meetings between US presidents and the Pope said that high-level Catholic staffers who expressed interest in attending the papal sessions were regularly accommodated. During his two equivalent sessions at the Vatican with Francis and his predecessor Pope Benedict, President Barack Obama was joined by his press secretaries, Jay Carney and Robert Gibbs, along with senior-level national security and West Wing aides.
Trump has demonstrated a vastly different management style in his West Wing, one that favors loyalty and blood ties over title or rank. Schiller, for example, holds the title of director of Oval Office operations -- a gatekeeper role that, in past administrations, has rarely extended past the Oval Office itself.
Staff intrigue has been a regular undercurrent of the Trump White House, both from outside the doors and behind the scenes. But rarely has the internal dynamic been on such obvious display than as Trump hops from nation to nation on his first international foray.
Much of Trump's senior-most aides traveled with him on his first jaunt abroad, packing the staff cabins on Air Force One for the 14-hour flight from Washington to Riyadh. For most, it was the longest stretch of time spent limited to each other's company.
Upon arrival, even lower-level staffers were treated to a royal welcome from King Salman and his royal court, a concerted effort by the Saudi government to flatter Trump and the decision-makers in his administration.
At an elaborate coffee ceremony inside the vast Royal Diwan, the internal hierarchy of Trump's West Wing was on plain view. Seated to the right of Trump, with the senior-ranking Saudi prince between them, was Ivanka, who along with husband Kushner has appeared in nearly every photo opportunity with her father. Other aides, including the chief of staff, were seated farther afield.
Trump's daughter and son-in-law have served as emissaries for their father, softening the rough edges of his governing style while lending his White House the air of a family business. Kushner played a chief role in planning Trump's foreign trip, acting as an interlocutor to foreign governments while helping to determine what deliverables Trump should seek at each stop.
In meetings with foreign leaders, Kushner has become a constant presence, from rapid-fire sessions with Arab Gulf leaders on Sunday to a day of shuttle diplomacy with Israeli Prime Minister Benjamin Netanyahu and Palestinian Authority President Mahmoud Abbas Monday.
Kushner even took the unusual step of issuing a written statement following Trump's stop in Riyadh, a valedictory display after a well-received visit to the Middle Eastern kingdom.
"The President asked us to plan a trip that would help unite the world against intolerance and terrorism and we have made great progress towards that goal in Saudi Arabia," Kushner wrote in his statement.
Typically when White Houses wish to issue a comment, it's attributed to the press secretary. But Spicer, who has become a late-night punchline at home for his strident defense of Trump, has been all but invisible abroad, declining to hold on-camera briefings and missing from top-level meetings.
Ivanka Trump, unlike ordinary senior advisers, has maintained her own schedule of events during Trump's trip, some of which have been covered by a separate pool of journalists and each eagerly consumed by local media.
After their highly public presence on the first three stops of Trump's trip, Ivanka Trump and Kushner are planning to return stateside on Thursday.
"The plan was always for them to go back to DC after Rome," a White House official said. "Jared helped plan and oversee the first part of the trip built around the theme of speaking to three of the world's biggest religions in Saudi Arabia, Israel and Rome."
Even the first lady, who back home has remained largely out of view, has stepped into public with new gusto on Trump's trip. At each stop she's split off from her husband's agenda to visit schools and hospitals, making waves with her fashion choices and, for the first time since he entered office, regular appearances away from the President.
Meanwhile, two of the highest-ranking Trump staffers returned home to Washington after the initial stop in Saudi Arabia. Both Priebus and Bannon had long planned to drop from the traveling presidential entourage early. But their absence has placed the inner West Wing dynamics in sharper relief.
Hicks and Scavino, both present for the meeting with Francis, are two of the President's longest-serving aides, both of whom joined Trump's campaign in its earliest stages. Each have played a central role in crafting his public image, through media management and Trump's active social media accounts.
It's all become something of a popularity contest inside the West Wing, playing out this week on the international stage. The week-long trip has only fueled speculation about a staff shakeup when the President returns to Washington. For some, the overseas journey could be their last in Trump's entourage, or not.
With this president, the only certainty is uncertainty.