Atletico were left frustrated in Moscow as their second-half pressure failed to produce a winner against Lokomotiv in Group A in a rare European game this season to be played before a sizeable crowd.
Atletico beat the Russians home and away in the group stage last season and went ahead in the 18th minute here when Hector Herrera's cross was headed in by Jose Maria Gimenez.
However, Lokomotiv were given the chance to equalise shortly after when Herrera was penalised for a handball in the box following a VAR review.
Anton Miranchuk converted the spot-kick to get the railway-backed club back on track.
They then soaked up pressure, as Angel Correa's long-range shot struck the bar before the interval and Guilherme saved superbly from Joao Felix after the restart.
Substitute Koke also headed against the woodwork for Atletico before Luis Suarez converted the rebound only to be flagged offside.
The result means Lokomotiv have now gone eight Champions League games without winning, and reigning champions Bayern can go five points clear of Atletico at the top of Group A if they beat Salzburg later.