The German champions produced a controlled performance to overcome Diego Simeone’s side, extending their unbeaten start in the league phase and returning to winning ways in the competition.
Atletico started brightly, with Julián Álvarez firing narrowly wide in the opening minutes. However, Bayern gradually took control of possession and began creating opportunities.
Lennart Karl threatened after being played through by his teammates, while Josip Stanišić also tested the home defence. Harry Kane came close to connecting with a dangerous cross from Laimer, but neither side could find the breakthrough before half-time.
The visitors eventually took the lead nine minutes after the restart. A hesitant clearance from Robin Le Normand allowed Karl to seize possession and lift the ball over the advancing Jan Oblak in the 54th minute.
The goal gave Bayern the advantage and forced Atletico to respond.
Simeone introduced Koke, Ademola Lookman and Kang-in Lee in an attempt to change the momentum, but Bayern continued to threaten.
Dayot Upamecano struck the crossbar before the visitors doubled their advantage in the 74th minute.
Kane provided the assist, finding Laimer inside the penalty area, where the Austrian defender finished confidently beyond Oblak to make it 2-0.
Bayern had another effort ruled out later in the match after a foul on Oblak, while Dávid Hancko fired over in stoppage time as Atletico struggled to find a way back.
The visitors ultimately secured all three points with a disciplined defensive display.
Bayern strengthen Champions League position
The victory takes Bayern Munich to eight points from their opening four league-phase matches, keeping them unbeaten in the competition.
For Atletico Madrid, the defeat represents a setback in their efforts to move up the standings, having been unable to make home advantage count against the Bundesliga side.
The match was also preceded by a minute’s silence in memory of CD Tenerife forward Jesús de Miguel, who died following an on-field collision during a Spanish second-division fixture.
Full-time result:
• Atletico Madrid: 0
• Bayern Munich: 2 (Lennart Karl 54', Konrad Laimer 74')