Heynckes, 72, also selected James Rodriguez to play alongside Javi Martinez and Arturo Vidal in midfield for the last-16 first leg, with Robert Lewandowski up front.
Ribery and Robben, veterans of Bayern’s last Champions League triumph in 2013, were left out as Heynckes switched captain Mueller to the right-hand side with French winger Coman on the left.
Ribery has only recently returned from a knee injury, but it is a surprise that Dutchman Robben, who scored the winner in the final five years ago, failed to make the starting XI.
Bayern are hoping to reach the quarter-finals for the seventh year in a row.
Besiktas coach Senol Gunes has brought winger Ricardo Quaresma, a Euro 2016 winnner with Portugal, and centre-back Domagoj Vida back into the starting line-up.
Defenders Dusko Tosic and Atinc Nukan, along with midfielders Veli Kavlak and Gokhan Tore, are all out injured for the visitors.
Canadian midfielder Atiba Hutchinson captains the side, which is spearheaded by Brazilian forward Vagner Love.
Bayern Munich (4-1-4-1)
Sven Ulreich – Joshua Kimmich, Jerome Boateng, Mats Hummels, David Alaba – Javi Martinez – Thomas Mueller (capt), Arturo Vidal, James Rodriguez, Kingsley Coman – Robert Lewandowski
Coach: Jupp Heynckes (GER)
Fabri – Adriano, Pepe, Domagoj Vida, Caner Erkin – Atiba Hutchinson (capt), Gary Medel – Ricardo Quaresma, Talisca, Ryan Babel – Vagner Love
Coach: Senol Gunes (TUR)
Referee: Ovidiu Hategan (ROU)
Would you like to place a soccer bet? Click here to get started in 3 easy steps.