The Portuguese forward converted a rebound from his own shot in the 48th minute to put the Spanish side on course for all three points after encountering stubborn resistance from their hosts in Russia.
Joao Felix – selected in an attacking XI that also included both Diego Costa and Alvaro Morata – was also involved in Atletico's second, scored by Thomas Partey.
Lokomotiv had played possum to perfection against Bayer Leverkusen last time out in Europe, enjoying just 22 per cent possession yet still managing to squeeze out a 2-1 win on the road.
They unsurprisingly opted to do the same again despite having home advantage against Atletico – and the policy paid off for the first half.
Atletico should have taken the lead in the 19th minute when Joao Felix's flick from a corner found an unmarked Costa, who somehow steered his left-footed volley over the bar from inside the six-yard box.
However, the deadlock was broken less than three minutes after the break, Joao Felix reacting quickly to capitalise on a second opportunity after goalkeeper Guilherme had saved his initial effort.
A second goal arrived 10 minutes later, Joao Felix's floated pass over a static defensive line allowing Costa to volley a pass across for the supporting Thomas to finish.
Jan Oblak produced a stunning save to keep out a crisp volley from Grzegorz Krychowiak as Atletico joined Juve, 3-0 winners at home against Bayer Leverkusen, on four points at the top of the table.
What does it mean? Atletico finally get into their stride
While this squad still feels like a work in progress after a stodgy start to their LaLiga campaign, Simeone will be pleased at how Atletico picked apart defensive opponents – as well as keeping another clean sheet.
Goals have been hard to come by in domestic action – they have managed seven in as many matches – but they have now scored four in Europe already, suggesting they could be set for another tilt at the trophy.
Price just right for Joao Felix
Utilised from the right flank but so often drifting inside, Joao Felix gave a demonstration of just why Atletico were willing to pay €126million to bring him in from Benfica. At 19 years and 325 days, he becomes the club's youngest scorer in the competition, a record previously held by Sergio Aguero.
How did Costa miss that?!?!
Costa remains stuck on one goal for the campaign following his shocking miss. It seemed nigh-on impossible to get the ball above the crossbar from close range, but somehow the former Chelsea striker managed it. At least it did not prove costly for his team, though.
Prior to the international break, Atletico head to Real Valladolid on Sunday. Lokomotiv, meanwhile, are in action on the same day, as they host Arsenal Tula. Both teams return to Champions League action on October 22.