The experienced coach feels the Roten lacked focus in the opening stages of the game and has set his sights on more silverware this season
Bayern initially struggled against the Serie A leaders as they seemed to lack focus but they dominated proceedings in the second half after making a number of tactical changes.
"It's not easy for players to be fully focused on a game after you've won the league just four days before," he told reporters at the post-match press conference.
"That appeared to be the case in the first 20 minutes when we often lost possession too easily and weren't fluent in our game going forward, but slowly we took control of the match and improved a lot in the second half.
"We discussed a few tactical matters at half-time. The tactical organisation had to improve and that's what happened in the second half. In the end we fully deserved the win."
Bayern have received their fair share of praise so far this season, yet Heynckes has stressed that they are not getting carried away as they are desperate to win more silverware after clinching the Bundesliga title at the weekend.
"We have received a lot of praise in the last few weeks. The positive aspect of this is that we recognised the praise but never let it influence our performances," he added.
"We are having a very good season with some fantastic displays. We are Bundesliga champions, but we still have other goals. We will see if we are on the same level as Madrid or Barcelona."
The draw for the semi-finals takes place in Nyon on Friday.