A Paco Alcaer brace and goals from Marco Reus and Jacon Bruun Larsen was enough to complete an impressive BVB comeback.
The victory now puts Favre's side to the top of the Bundesliga, and the Swiss head coach could not hold back his delight for his players.
"The goals we conceded were unnecessary. For the first one, we made too many mistakes. We can't allow that to happen", he told the club's website.
"The second came from a corner where we didn't anticipate the second phase well after a clearance. That cost us two goals.
"But you always need to believe in yourselves. A goal changes everything. We showed our spirit again. There were a lot of emotions at the end.
"Winning 4-2 after being 2-0 down is super. Leverkusen could've scored a third, but we controlled the match well in the second period, we played better then. It's very nice to be at the top of the table. It's been a good start," he added.