Hannover keeper Philipp Tschauner was in inspired form in the first half to deny Niklas Süle, Thiago Alcantara and Sandro Wagner (twice) as the home side made it to half time unscathed.
Heynckes was forced to call on the big guns, bringing on both Thomas Muller and Robert Lewandowski after the interval. Both players scored before Sebastian Rudy added a late third to seal a pleasing away win.
"We're very satisfied," Heynckes told Bayern's official website. "Taken altogether we played excellent football. 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."
Heynckes made seven changes in total as key men were rested ahead of Bayern's Champions League semi final against Real Madrid. The first leg takes place at the Allianz Arena on Wednesday, and Heynckes was pleased to keep the momentum going ahead of that game.
"It's always important to win in the league when the Champions League awaits you," he said.
Wednesday's match will go a long way to determine whether Bayern can replicate the treble season that Heynckes masterminded in 2012-13. They have already won the Bundesliga title and will be expected to beat Eintracht Frankfurt in next month's DFB-Pokal final.
Real Madrid have eliminated Bayern in two of the last four seasons, so the Bavarian club will be out for revenge against the current European champions.