Bayern Munich were struggling to get in to the game thanks to a stubborn AEK defence for much of the game, and it took them until the 61st minute of the encounter to finally break the deadlock.
The ball was pulled back to Arjen Robben who drove the ball towards goal, with a defender managing to get a block in.
The ball rebounded to Javi Martinez, who did exceptionally well to acrobatically volley the ball in to the back of the net from close range and give Niko Kovac a much-needed foothold in the game.
Within two minutes the lead was doubled, thanks to a good effort down the left flank which led to Serge Gnabry feeding Rafinha.
The Brazilian managed to slot the ball across the six yard box first-time, to find Lewandowski for an easy tap in.