Back-to-back Group D defeats left Atletico needing to beat already-eliminated Lokomotiv at Wanda Metropolitano on Wednesday to make certain of progression alongside Juventus.
Kieran Trippier missed a penalty with 114 seconds on the clock but Joao Felix settled the home side's nerves and ended their recent goal drought by converting from the spot 15 minutes later.
Alvaro Morata had a goal ruled out for offside but Felipe added a second early in the second half for Atletico, who are in the hat for Monday's knockout-stage draw at the expense of Bayer Leverkusen as they were beaten by group winners Juve.
Anton Kochenkov brought down Joao Felix inside the opening minute of his first Champions League appearance, but the goalkeeper got a hand to Trippier's attempt to help it onto the post.
Atletico made amends when VAR adjudged Rifat Zhemaletdinov handled Vedran Corluka's clearance, with Joao Felix picking out the bottom-left corner from the spot.
Morata tucked Angel Correa's pass away from Kochenkov, only for the video technology to this time work against Atletico as the striker's heel was deemed to be offside.
Any hope Lokomotiv had of dodging a fifth successive Group D loss were ended by centre-back Felipe, who converted Koke's cross with a side-foot volley at the near post.
Morata headed over from a good position with 18 minutes to play, though it did not matter as Diego Simeone's side saw things through.
What does it mean?
Atletico were involved in a straight shootout with Leverkusen for second place behind Juve.
Leverkusen had to beat the Italian champions to have any hope of progressing but lost 2-0 at home, meaning Simeone's men finished four points better off.
Joao Felix shows Trippier how to do it
Atletico entered this match without a goal in three outings and their barren run was prolonged by Trippier's penalty as Kochenkov atoned for his foul.
It was hit at a good height for Kochenkov, whereas Joao Felix – who also won the first penalty – picked out the bottom corner with his attempt and left his opponent rooted to the spot.
Lokomotiv lack impetus
Three-time Russian Premier League champions Lokomotiv showed a serious lack of attacking threat, managing just three across the 90 minutes, one of those on target.
They end 2019 with one win in their last 11 matches, losing four in a row.
Atletico have a home league meeting with Osasuna on Saturday. Lokomotiv do not have a competitive game until late February when Russian Premier League action resumes.