Sane has had a tough time since joining Bayern from Manchester City, being restricted to just five Bundesliga starts.
He was once again named on the bench for Sunday's (AEDT) trip to the BayArena but was introduced just after the half-hour mark for the injured Kingsley Coman.
However, the Germany international lasted only 36 minutes on the field before being taken off for Jamal Musiala with the game poised at 1-1 and Bayern chasing a goal.
Sane cut a frustrated figure as he made his way back to the bench but head coach Hansi Flick felt he had no other choice but to make the tough call.
"It wasn't a punishment," he said after the match. "I had to make a sub, and the options were either Thomas Muller, Serge Gnabry or Leroy.
"Thomas is indispensable for our system, Serge really got into the game in the second half. So I had to sub Leroy off.
"Ultimately, it's about the success of the team above the individuals. We support Leroy in every way possible."
Sane lost possession nine times, completed 15 of his 19 passes (78.9 per cent) and conceded two fouls, which was more than any other Bayern player.
But Muller, who by comparison was successful with 38 of his 52 passes (73.1 per cent) and lost possession a joint team-high 20 times, leapt to his team-mate's defence.
"Hansi must have had his reasons," Muller said of Sane's withdrawal.
"Personally, I really enjoy playing with Leroy and I think we had more offensive moves down the right when he came on.
"I don't think it will be that long until we start talking about Leroy in a different way. He is very close to breaking through.
"He shouldn't get frustrated by this but motivated. It doesn't make it any easier that we're struggling a little as a team at the moment."
Sane creates an average of 0.7 big chances per 90 minutes he plays in the Bundesliga this season, which is bettered only by Coman (1.07) among Bayern players to have featured at least six times.
Only Douglas Costa (2.97) and Musiala (3.71) have completed more dribbles per 90 minutes than Sane's 2.45, meanwhile, and sporting director Hasan Salihamidzic is happy with the ex-City attacker's displays since recovering from a long-term lay-off.
"The guy is really a top player, he was injured for a long time," he said. "He also wants more from himself.
"The team will help him. I'm sure and I totally believe in him. He has qualities that he will hopefully show us in the first game of the new year."
Lewandowski scored twice against Leverkusen, including a 93rd-minute winner, after Patrik Schick had given the home side the lead.
The Poland international, whose 17 goals after 13 Bundesliga matchdays is a joint-record alongside Gerd Muller, also predicted a brighter future for Sane.
"He needs a bit of time," Lewandowski said. "Next year I'm sure he'll show his quality. I'll keep my fingers crossed for him – he's a great guy.
"He knows himself that he can benefit from a short break and we will need him going forward."
Leader Bayern has trailed 1-0 in each of its past seven Bundesliga games – its longest ever such run – but will take a two-point lead into the mid-season break after this latest fightback.