The stalemate left Bayern top of the Bundesliga on 69 points from 29 games, eight more than closest rivals RB Leipzig who booked Champions League football next season for the first time in the club's history with a 4-0 home win over Freiburg.
Still reeling from Wednesday's 2-1 home defeat by holders Real Madrid in their Champions League quarter-final first leg, Bayern again lacked the cutting edge without Lewandowski who is struggling to recover from a shoulder injury.
The prolific Pole has scored 38 goals in 40 games in all competitions this season and Bayern could have done with his lethal finishing against Leverkusen as they missed a barrage of gilt-edged chances.
Arturo Vidal, Kingsley Coman, Thiago Alcantara and Thomas Mueller, playing as the lone striker in a makeshift formation, all came close before the home side had their Croatian defender Tin Jedvaj sent off on the hour for a second bookable foul.
Substitute Philipp Lahm missed Bayern's final and best chance in the 85th minute, when he dragged his shot wide from five metres with only goalkeeper Bernd Leno to beat after a good run and cross by Mueller.
Leverkusen, who have won only one of their last eight league games, moved one place up to 11th on 36 points from 29 games.
(Writing by Zoran Milosavljevic; Editing by Ian Chadband)
