Joao Felix put Atletico Madrid in the driving seat early in the second half of a tight game, sliding to knock the ball in on the rebound after his first shot had been saved by the hosts' goalkeeper Guilherme.
READ MORE: Cute photos of Ghanaian footballers kids
Atletico had drawn blanks in three of their previous five games but a goal finally arrived when Felix showed hunger to race into the area and meet a low cross from Morata, and then follow up his shot to score.
Before Thomas Partey doubled the lead finishing off a pass from Diego Costa after a lovely chipped ball from Felix, who became the fourth-most expensive player of all-time when he joined from Benfica in July.
The win took Atletico into second place in the group on four points, the same number as leaders Juventus who beat Bayer Leverkusen 3-0 and have a better goal difference.
Atletico had produced a gutsy comeback to draw 2-2 at home to Juventus two weeks ago and although there was less drama in this victory, Diego Simeone's side always looked in control in the Russian capital.
They should have taken the lead early in the first half when a flicked header from Felix made its way to an unmarked Diego Costa at the far post, who somehow missed the target with a gaping goal in front of him.
Alvaro Morata, who was back in the team after being suspended for Saturday's goalless draw against Real Madrid, also had a chance to put Atletico ahead before the break but was thwarted by Guilherme.