Josip Ilicic put Atalanta ahead in the 12th minute before Ronaldo scored the equalizer in the 45th minute at Gewiss Stadium.
In the second half, Duvan Zapata made the score 2-1 in the 66th minute, but Ronaldo scored his second goal in stoppage time, leading his team to salvage a point in Italy.
Villarreal beat Young Boys 2-0 in another Group F clash.
Manchester United and Villarreal have seven points each with Atalanta collecting five points in the group.
Young Boys sit at the bottom with three points.
Tuesday's results in Champions League:
Group E
Bayern Munich - Benfica: 5-2
Dynamo Kyiv - Barcelona: 0-1
Group F
Atalanta - Manchester United: 2-2
Villarreal - Young Boys: 2-0
Group G
Wolfsburg - Salzburg: 2-1
Group H
Malmo FF - Chelsea: 0-1
Juventus - Zenit St. Petersburg: 4-2
