The Colombian international, who is on loan at the Bundesliga outfit from Real Madrid, was a doubt for the clash, which could end up being a formality for Bayern.
The five-time European champions already have a 5-0 lead from the first leg at the Allianz Arena.
Heynckes has made just two changes to the team that romped to a 6-0 win over Hamburg at the weekend.
Besiktas: Zengin; Gonul, Uysal, Medel, Erkin; Ozyakup, Arslan; Quaresma, Lens, Pektemek; Vagner Love
Subs: Ramirez, Adriano, Babel, Negredo, Hutchinson, Aksoy, Souza
Bayern Munich: Ulreich; Rafinha, Boateng, Hummels, Alaba; Martinez; Muller, Vidal, Thiago, Ribery; Lewandowski
Subs: Starke, Wagner, Sule, Rodriguez, Bernat, Rudy, Kimmich