- Anton Miranchuk (79' Pen)
- Mergim Berisha (28', 41')
- Karim Adeyemi (81')
Salzburg were rewarded for their early domination in the 28th minute when Enock Mwepu's deflected shot fell kindly to Berisha, who converted from close range, minutes after he had a goal ruled out for offside.
Jesse March's side doubled their lead 13 minutes later when Sekou Koita capitalised on a poor clearance from Slobodan Rajkovic and played in Berisha, who rifled a low shot past Lokomotiv keeper Guilherme for his fourth goal in five Champions League games this season.
Yet substitute Karim Adeyemi restored Salzburg's two-goal lead two minutes later, profiting from another defensive error and firing into the bottom corner.
Salzburg host Atletico in their final group game next week and can qualify for the knockout stages with a win over Diego Simeone's side.