Markovic was expected to miss the Turkish Cup final against Galatasaray tonight in Antalya but passed a late fitness test and will make the trip.
The Serbian international has struggled for regular playing time this season due to multiple injuries throughout the league campaign.
Fenerbahce finished the league campaign as runners-up and will compete in the Champions League next season.
Full Fenerbahce squad:
Fabiano Ribeiro, Ertuğrul Taşkıran, Erten Ersu, Anıl Demir, Bruno Alves, Simon Kjaer, Michal Kadlec, Abdoulaye Ba, Hasan Ali Kaldırım, Karahan Yasir Subaşı, Gökhan Gönül, Şener Özbayraklı, Mehmet Topal, Josef De Souza, Ozan Tufan, Diego Ribas, Raul Meireles, Uygar Mert Zeybek, Ramazan Civelek, Melih Okutan, Alper Potuk, Volkan Şen, Lazar Markovic, Luis Nani, Jose Fernandao, Robin van Persie.