The veteran coach brought up the landmark thanks to Wednesday's routine 3-1 win at Besiktas, wrapping up an 8-1 aggregate victory that booked a place in the quarter-finals.
Heynckes was appointed by Bayern for his fourth spell in October following the sacking of Carlo Ancelotti, the Bundesliga side winning each of his European games in charge since then.
And as Heynckes led Bayern to the Champions League title in 2013 before ending his third period in charge, he has now won 11 successive matches in the competition.
The 72-year-old is yet to sign a contract extension, with his deal at Bayern set to expire at the end of the campaign.
However, Heynckes has hinted he would be willing to stay at the club for at least one more season.