Bayern were a threat every time they had the ball, however, and their second arrived shortly after the interval when Gokhan Gonul turned into the back of his own net from close range.
Heynckes' men could claim the Bundesliga title at the weekend if results go their way and they remain on track for another treble, the veteran coach having won the Champions League among three trophies before departing Bayern at the end of his third spell in 2013.
Besiktas' best chance of the first period fell to Ricardo Quaresma in the 38th minute, but the Portuguese saw his free kick just miss the crossbar.
Bayern extended their lead moments after the start of the second half when Turkey global Gonul flicked the ball into his own net from a Rafinha cross.
It extended coach Jupp Heynckes' record to just one defeat in 28 matches and took Bayern's tally in this season's competition to 21.
Wagner, who joined Bayern in the January transfer window, has already scored in the Champions League qualifying rounds for Hoffenheim this season as well as in the Europa League.
Besiktas are unbeaten in their last six Champions League home games, though five of these have ended as draws (W1).