Cristiano Ronaldo was their match-winner again, heading into the 81st minute as the Red Devils fought back from a two-goal deficit.
First-half goals from Mario Pasalic and Merih Demiral had Gli Orobici two for good at the break, leaving the Red Devils on the brink of another defeat.
However, the side bounced back spectacularly in the second-half.
Marcus Rashford, in the 53rd minute, halved the deficit before Harry Maguire leveled the proceedings a while later.
The match was still headed for a draw, but cometh the hour, cometh Ronaldo. He rose the highest to meet a fabulous cross from Luke Shaw and powered home a crisp header.
Manchester United fought back from the jaws of a defeat and now climb to the top of Group F, condemning the Italian side to second.
Here are the
Player ratings for Manchester United
David de Gea - 8/10
There was nothing he could do about either of Atalanta's goals. But the Manchester United custodian made two fine saves in the second-half to burnish his world-class credentials.
Aaron Wan-Bissaka - 6.5/10
Atalanta's marauding attackers had pegged him back but he did no wrong defensively. He also helped in attack in the second half when Manchester United pushed for the win.
Victor Lindelof - 6.5/10
The Swede was generally okay but Davide Zappacosta sure gave him a nervy moment in the second-half. He was also beaten by Duvan Zapata but was saved the blushes due to a good save by De Gea.
Harry Maguire - 7.5/10
The Manchester United custodian made up for a pathetic opening half with massive improvements after the break. Not only was he solid defensively, but also got his side level with a superb equalizing goal.
Luke Shaw - 7.5/10
His assist for Ronaldo's winning goal was one for the ages, perfectly finding the Portuguese star amid a sea of white shirts. That cross was a work of art, really.
Scott McTominay - 7.5/10
He was vital in the first-half, making an important interception and blocking each to save Manchester United's beacon. In the second-half, McTominay saw a shot come off the post.
Fred - 7/10
An excellent game for the Brazilian, who knitted passes together and just got better after the break.
Mason Greenwood - 6/10
Scorer of a beautiful goal against Leicester at the weekend, Greenwood had a poor game tonight, failing to get a single shot away.
Bruno Fernandes - 7/10
The Portuguese too had a horrific first-half, struggling to retain possession and misfiring awfully in front of goal, but saved face with a fine assist for Rashford.
Marcus Rashford - 8/10
He missed three good chances in the first-half but atoned for those misses with a goal which sparked Manchester United's comeback. Rashford now has seven goals in seven group-stage matches.
Cristiano Ronaldo - 8/10
A very good all-round performance capped off with a peach of a header to win it for Manchester United. Three goals in three games for Mr. Champions League now.
Paul Pogba - 7.5/10
His arrival immediately made things better for Manchester United in midfield as they wrestled back control.
Edinson Cavani - 6/10
El Matador came on to add more firepower to Manchester United's play but struggled to get serviced. Nevertheless, bagged an assist for Maguire.
Jadon Sancho - 5/10
Another no-show from Sancho, whose Manchester United career is turning into a nightmare.
Nemanja Matic - N/A
ALSO READArticle Continues below
The game was almost up by the time the Serb was subbed.