The 57-year-old is in London to record a special song for Prince Harry's Invictus Game Foundation for military veterans.
He told radio station Talk Sport on Wednesday he had been in his hotel bar on Monday as had the Bayern players.
"I was minding my own business in the bar," Bon Jovi said.
"And the team were in there the night before last (Monday) and how they, on the power of whisky and beer, overpowered Chelsea last night doesn't say much for Chelsea's drinking habits either."
Jovi, whose biggest hit was the 1987 single 'Livin On A Prayer', joked his indiscretion might get some of the players into hot water.
"The Bayern guys were certainly sipping whisky and having a good ol' time -- and they went and shellacked Chelsea," said Jovi.
"I am going to get everyone in trouble."
The second leg takes place on Wednesday March 18 at the Allianz Arena.