"Luther Strange has been shooting up in the Alabama polls since my endorsement," Mr Trump wrote in one now-removed post.
He campaigned for Mr Strange, but could not save him from defeat to ultraconservative firebrand Roy Moore.
The underdog's victory has sent shockwaves through Washington.
Things Republican Roy Moore believes
In one now-deleted Tweet, the president said Mr Strange "will never let you down!" according to news website ProPublica, which documents Mr Trump's posts.
In another, the president said "vote today for 'Big Luther'".
Early on Wednesday, Mr Trump changed his tune to congratulate Mr Moore on his victory.
"Sounds like a really great guy who ran a fantastic race. He will help to #MAGA!" he tweeted, referring to his "Make America Great Again" catchphrase.
The Republican president has been known previously to occasionally delete tweets, most often replacing them after correcting spelling errors or other mistakes.
Some watchdog groups have criticised the deletions, saying that the tweets are government records that must be preserved for the historical record.
Mr Moore rode a wave of support in the Republican primary from the same grassroots conservative movement that helped elect Mr Trump.