MLB said Rose, 74, was informed of Manfred's decision verbally and in writing that his application has been denied.
Manfred wrote in his decision, which was released by MLB on Monday, that consideration for Rose to be reinstated "falls well short" of the requirements needed.
"Mr. Rose's public and private comments, including his initial admission in 2004, provide me with little confidence that he has a mature understanding of his wrongful conduct, that he has accepted full responsibility for it, or that he understands the damage he has caused," Manfred wrote.
Rose, who is MLB's all-time hits leader with 4,256, was banned for life in August 1989 for betting on baseball. Rose denied betting on baseball then and continued to deny it for 14 years. In 2004, Rose admitted in his autobiography, "My Prison Without Bars," that he did bet on baseball while managing the Cincinnati Reds.
Pete Rose attorney Ray Genco expressed disappointment at the ruling and said Rose will address the media Tuesday at 11 a.m. Pacific Time (2 p.m. Eastern Time).
He said that Rose had met the standard put forth by Bart Giamatti who, during his brief tenure as MLB commissioner (he died a few months after taking office in 1989), helped negotiate Rose's voluntary departure from baseball.
"While we may have failed at our task of presenting all the facts to the (current Commissioner Rob Manfred) demonstrating how Pete has grown and changed over the past three decades, Pete indeed has meaningfully reconfigured his life -- the standard laid out (by) Commissioner Giamatti," Genco said.
"Pete's fall from grace is without parallel. He recognizes that it was also of his own making.
"As such, Pete seeks to be judged not simply by the mistakes of his past -- but also by the work he has done over the last three decades in taking responsibility for his actions -- constantly working to remain disciplined, compassionate and grateful.
"Pete regards the institution of the game as what matters most. Therefore, he will continue to do all that he can to honor its greatness- and remain its most enthusiastic fan."
Manfred made it clear that his decision on Rose has no impact on his eligibility for the National Baseball Hall of Fame, which, notably, is not run by MLB.
"It is not a part of my authority or responsibility here to make any determination concerning Mr. Rose's eligibility as a candidate for election to the National Baseball Hall of Fame," Manfred wrote. "In fact, in my view, the considerations that should drive a decision on whether an individual should be allowed to work in Baseball are not the same as those that should drive a decision on Hall of Fame eligibility."
Manfred also wrote that Hall of Fame policy is an entirely different determination and that his only concern is protecting the integrity of play on the field through appropriate enforcement of Major League Baseball rules.
"Any debate over Mr. Rose's eligibility for the Hall of Fame is one that must take place in a different forum," Manfred wrote.
On February 26, Rose's attorneys advised Manfred of Rose's request for reinstatement, saying that Rose had accepted responsibility for his mistakes and their consequences and that he was sorry for betting on baseball.
Manfred said he requested his staff conduct a comprehensive review of all materials concerning the Rose case, which included John Dowd's report from 1989 -- Dowd served as special counsel to three commissioners of Major League Baseball in the investigations of Pete Rose, George Steinbrenner, and others. The materials also included a copy of a notebook that apparently shows records of bets placed in 1986 by a man named Michael Bertolini, who allegedly placed bets on behalf of Rose. The notebook's existence was revealed by ESPN in June this year, suggesting Rose may have bet on baseball when he was an active player, contradicting Rose's story, according to reporting by ESPN.
Rose and Manfred met on September 24. In that meeting, Rose told Manfred that he bet "extensively" on Reds games in 1987. However, Manfred wrote, Rose said he could not remember facts from the Dowd Report that showed he bet on baseball as a player.
"He made assertions concerning his betting habits that were directly contradicted by documentary evidence (the Bertolini Notebook) secured by my office following the publication of the ESPN story on June 23, 2015," Manfred wrote, "And, significantly, he told me that currently he bets recreationally and legally on horses and sports, including Baseball."