Goals from Thomas Muller, Robert Lewandowski and Sebastian Rudy gave the Bavarians victory at the Niedersachsenstadion, leading Heynckes to highlight the positivity of the victory heading into a Champions League semi-final clash against Real Madrid.
"We're very satisfied. Taken altogether we played excellent football," the outgoing Munich coach told reporters.
"The team are top fit, no matter who's playing, regardless of the position. It's important that we keep up our rhythm and don't ease off and that we can still improve.
"It's always important to win in the league when the Champions League awaits you."
Lewandowski's strike in the game made the Poland international the most prolific non-German for a single club in Bundesliga history.