Ronaldo scored his ninth goal in 11 games for United as he bagged both equalisers in the game.
The most important equaliser came in stoppage time when he volleyed home to snatch a point on a night where United were dreary.
For the first equaliser - which came in the first half - the substitute, Mason Greenwood, spotted Bruno Fernandes’ intelligent run into the 18-yard-box and the Portuguese midfielder brilliantly found Ronaldo with a backheel pass for Ronaldo to slot past Juan Musso.
Atalanta took the lead early in the match, like they did at Old Trafford a fortnight ago, through Josep Ilicic. Ilicic’s effort from outside the box beat a weak-handed-diving David De Gea. To be fair to the Spanish goalkeeper, it was his first mistake of the season, but he shouldn't be beaten in that fashion.
United now share pole position with Villarreal, a team they will have to travel to later in the month. With just two games remaining in the group stages, only two points separate top and third.
Story of the game
As United continued in their new formation with three at the back, they saw a lot of the ball in the opening stages of the game. Ronaldo had a shot from distance in the opening minute and Scott McTominay’s strike from inside the box was deflected and rebounded off the post.
But it was Atalanta who took the lead in the 12th minute when Zapata picked up the ball from the left and cut the ball back to find Ilicic. The Slovenian international then struck the ball first time right at David De Gea who made his first mistake of the season as the ball trickled under his right hand.
The hosts looked to double their lead through Zapata as they really took control of the game. A deep ball from Davide Zappicosta over the top of Harry Maguire found Zapata in behind but he blasted his effort over the bar.
Atalanta should have been more than one goal to the good after half an hour played and United had only themselves to blame. Zapata once again should have scored. This time, Paul Pogba gave the ball away in his own 18-yard-box and if it wasn’t for a jumping/diving header from Eric Bailly, Zapata would have smashed it into the top left corner.
And with that, came United’s equaliser. Fernandes and Ronaldo combined to snatch an equaliser in added time of the first half. It started with the substitute, Greenwood, who found the darting run of Fernandes into the box. Fernandes then backheeled the ball into the path of Ronaldo who buried it home.
But it was Atalanta again who came out the better side in the second half. Finally, Zapata got his goal. This time, you could blame either De Gea or Maguire…or both. Neither wanted to come and win the ball, Zapata took control and finished past De Gea.
After an initial look at the goal, it looked as though Zapata was offside. The linesman’s flag went up, however, VAR took a look at it and awarded the goal after a lengthy wait.
Had it not been for Bailly - who was arguably United's man of the match - Atalanta could have gone on to score at least two more goals. For a defender who has seen a lack of minutes on the pitch this season, his performance was the standout.
To demonstrate the desperation of Solskjaer, he brought on Donny van de Beek and Jadon Sancho with less than ten minutes to play. Both have endured the polar opposite of what they thought their United careers would look like.
Ronaldo then popped up at the death with a fine volley past Musso to steal a point to take back to Manchester.