The German champions went behind early to an own goal by Alphonso Davies and it took until the final ten minutes of the game before they could muster a response with goals from Serge Gnabry and Thomas Muller saving Kovac’s blushes.
Bochum are second from bottom in the second-tier of German football and have not won a home game since May but were on the brink of eliminating the holders from the competition.
"It was all wrong for 60, 70 minutes," an unhappy Kovac said.
"The fact that we played so many bad passes, in my opinion, has something to do with the attitude ... it has nothing to do with tactics. It has to do with the attitude.
"There were too many players who played bad passes."
Kovac had to summon Philippe Coutinho, Robert Lewandowski and Thomas Muller from the bench in the second half to salvage something from the game, and the Croatian tactician expressed gratitude to his substitutes for delivering for him.
"After Philippe Coutinho and Thomas Muller came on, things improved," he said.
"And in the end we got that little bit of luck against Bochum, who really played so well."
Bayern return to Bundesliga action against Kovac’s former club Eintracht Frankfurt at the weekend as they look to return to the top of the table, which is currently occupied by Borussia Monchengladbach.
