Lewandowski has already bagged 10 goals in six Bundesliga games this season and showed why he is one of the world's most-feared strikers as he beat Lloris with a shot on the turn seconds before the halftime interval.
Having missed games against Aston Villa, Manchester City and Newcastle, Alli was introduced on the hour for the 2-2 draw at Arsenal on September 1. Moussa Sissoko played a wonderful threaded pass through to Son, who got the better of Neuer and struck it into the far corner as Tottenham broke the deadlock in north London.
Last week's League Cup exit against fourth-tier Colchester was a low point and Pochettino blamed that setback on "different agendas in the squad".
That Alli delivered a limp performance in Tottenham's shock penalty shoot-out defeat suggested Pochettino had been correct to use his playmaker so little.
"We should have decided the game earlier for ourselves", Neuer fumed as Bayern squandered chances before Robert Lewandowski scored what proved to be the victor with his 10th goal in six league games. We were way too passive, we didn't show enough presence.
Lewandowski was played in by Philippe Coutinho and finished in deadly fashion and with Tottenham's defence AWOL again, Gnabry put Niko Kovac's team in seventh heaven.
Although Alli's assist led to Tottenham's dramatic semi-final second leg victor for Lucas Moura at Ajax, that was a rare highlight.
The loss was Tottenham's largest defeat in Champions League history, and was the first time they conceded seven goals at home in any major competition.
Tuesday's match had been billed by many as a clash of the world's two best centre-forwards - Kane vs Lewandowski - it's safe to say, the Poland worldwide won.
"This is what every manager wants to do be successful in the Champions League", he added.
Serge Gnabry scored two goals in two minutes for Die Roten, with a wonderful piece of dribbling and a neat finish giving the visitors in firm control of the affair in style.
While Alli has been struggling, Tottenham have found themselves in distress as well, rocked by the unsettling circumstances surrounding their failure to offload Christian Eriksen, Jan Vertonghen, Danny Rose and Victor Wanyama in the close-season.
Pochettino said he would like to keep Vertonghen but that he was not part of the negotiations.
Saturday's spirited 2-1 win over Southampton, achieved despite the dismissal of Serge Aurier, was a step in the right direction.
Bayern look like a new animal this season and if Tuesday night is anything to go by, they're going to take some stopping. We are not going to fix anything by shouting. But after 30 minutes, my feeling was good.