Bayern manager made one change from the victory over Wolfsburg over the weekend, as David Alaba made way for Rafinha at left-back while Franck Ribery was left out of the match day squad completely.
The Bundesliga champions carved out a couple chances in the opening exchanges, with Lewandowski going close with a headed effort after 12 minutes.
The chances continued to fall for Bayern and Thiago should have broken the deadlock in the 27th minute, but the Spaniard failed to hit the target from inside the box.
Bayern had another chance to break the deadlock after 38 minutes as James Rodriguez played Serge Gnabry, who rifled his effort into the side-netting.
It took a while for Bayern to get the opening goal but it eventually arrived on 61 minutes via an unlikely source, with Javi Martinez firing home close range.
The lead was doubled moments later through Lewandowski, who turned home Rafinha's low cross in the box.
The Bavarians pushed for more goals as the second half went on, and Lewandowski went close in the 78th minute with acrobatic effort that sailed just wide of the mark.
Vasilios Barkas ensured the game ended 2-0 as the AEK shot-stopper produced a superb save to deny Leon Goretzka in the box, as the Bundesliga giants walked away with three points.