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No explanation was immediately forthcoming for the decision to drop former Real Madrid and Arsenal star Ozil from the club's plans.
The same action was taken regarding Turkey midfielder Ozan Tufan.
Fenerbahce issued a statement that read: "Our football A team players Mesut Ozil and Ozan Tufan were excluded from the squad as per the decision taken."
Ozil was substituted at half-time in Fenerbahce's game against Konyaspor on Monday (AEDT), with the team trailing 1-0 at that stage. It recovered to win 2-1, with Tufan entering the game late on as a substitute.
In an Instagram post on Thursday (AEDT), Ozil revealed he had taken a short getaway since that game, with the 33-year-old accompanying his message of "Back in Istanbul after 3 days off" with a picture of himself on an aeroplane.
That followed coach Ismail Kartal praising the squad after the Konyaspor game and announcing all of his players, aside from those going away on international duty, could have a three-day break.
Former Germany international Ozil was a star-name signing when he arrived from Arsenal in January 2021, having fallen out of favour with the Premier League club. Tufan spent the first half of this season at Watford.
Fenerbahce sits third in the Turkish Super Lig this season, two points behind Konyaspor but 17 adrift of runaway leader Trabzonspor.