The two have both pumped political capital into helping Sen. Luther Strange survive a stiff challenge from his own party.
They'll have to wade even deeper in the race if Strange is to win a one-on-one contest against the controversial, twice-ousted former state Supreme Court chief justice Roy Moore, who got 39% of the vote to Strange's 33% in Tuesday's primary, pushing the two into a September 26 runoff.
On Wednesday morning, Moore was already trying to drive a wedge between Trump and McConnell as he portrayed Strange as McConnell's lackey.
On morning radio shows, including WAPI 99.5 in Birmingham, Moore pointed to Trump's call for the Senate to abolish the filibuster
and drop to a simple 51-vote majority to pass legislation.
Strange signed an April 7 letter supporting the filibuster -- backing McConnell's desire to keep it in place.
Moore seized on that, casting it as a rebuke of Trump's agenda. By keeping the filibuster in place, Moore said, Strange "doesn't support getting stuff done."
For Trump and McConnell, pushing Strange through his matchup with Moore means setting aside differences that have flared in recent days.
Their differences came into public view when Trump lambasted McConnell's failure to shepherd a health care bill through the Senate
. On Wednesday, McConnell implicitly criticized Trump's response to white supremacists in Charlottesville, Virginia. The two will now be involved in a push to beat an end-of-September deadline to fund the government, with Trump demanding backing for his border wall.
Trump and McConnell both pumped political capital into an effort to help Strange, who was appointed in February to fill Attorney General Jeff Sessions' former seat, survive the primary against Moore and Rep. Mo Brooks, who finished with 20% support.
Trump endorsed Strange. And McConnell-aligned groups spent more than $4 million attacking his primary foes with television ads.
For McConnell, the race is a prime example of his policy of sticking by incumbent Republican senators, even in the face of challenges within their own party. He is also backing Nevada Sen. Dean Heller and Arizona Sen. Jeff Flake
, two endangered incumbents already facing primary challenges in the 2018 midterms.
But across Alabama, Republican voters said it was Trump's support -- including two endorsements on Twitter and a robo-call -- that drove them into Strange's camp.
And on Twitter Wednesday morning, Trump claimed credit for support snowballing toward Strange.
"Wow, Senator Luther Strange picked up a lot of additional support since my endorsement. Now in September runoff. Strong on Wall & Crime!" Trump tweeted
Headed into the runoff, the biggest question is what Trump will do to support Strange.
Two tweets and a robo-call require little effort from the White House. But Alabama is an important state to Trump's political rise. An August 2015 rally here, which drew tens of thousands, was a national eye-opener early in his campaign. A trip to the state to support Strange, or cutting an ad on his behalf, could be a major boost. And a loss by the Trump-backed candidate would be an embarrassment for the President.
Still, in his first tweet about the race Wednesday morning, Trump appeared to hedge
"Congratulation to Roy Moore and Luther Strange for being the final two and heading into a September runoff in Alabama," he tweeted. "Exciting race!"