The European champions face Tigres in the final on Thursday after the Mexican club saw off Brazilian giants Palmeiras in Sunday's other semi-final.
Lewandowski gave Bayern the lead with just 17 minutes gone at the Ahmad Bin Ali Stadium, a host venue for the 2022 World Cup in Qatar.
Al Ahly did their best to keep Bayern out but they were second best for large spells of the match. Their best chance was perhaps a Mohamed header that Neuer got down and gathered easily.
Roca then had a shot that went just wide before Lewandowski had a chip but the onrushing El Shenawy did enough to put him off. Davies had an effort 5 minutes before half-time but his shot whistled wide.
The best chance in the second-half fell for Muller but his header was tipped over the bar by the active Al Ahly keeper.
All hopes of an Al Ahly comeback were put to bed in the 85th minute when Lewandowski headed home a Leroy Sane cross to book Bayern's place in the final.
Al Ahly will face Palmeiras in the 3rd/4th play-off.
February 8, 2021