The 46-year-old Turkish coach returns to the Istanbul club from Kasimpasa, having previously served as Fenerbahce's interim manager in 2021. The appointment was confirmed by the club on Tuesday.
Belözoglu takes over after Kuyt was placed in temporary charge following the departure of the previous head coach. The Dutchman oversaw just one match, a home defeat against Göztepe last weekend.
Fenerbahce are due to face Liverpool in the Champions League on Wednesday, meaning Belözoglu's appointment comes immediately before a major European fixture.
The former midfielder knows the club well. Before his previous spell as interim coach, he worked as Fenerbahce's sporting director and was part of the squad that won the Turkish league title in 2014.
Kuyt's future at the club remains unclear. The former Liverpool forward has expressed a desire to remain in Istanbul, although it is not yet known whether he will be offered a position on Belözoglu's coaching staff.
"One thing I know for sure: I'd like to stay here. I think the most important thing is that Fenerbahce makes the right choices for its future," Kuyt told NOS.
The 46-year-old also made clear his commitment to the club, despite the uncertainty surrounding his role.
"I am willing to give anything for this club, but the decisions are made by other people. I think this is a fantastic club, I am having a great time," he said.
Kuyt and Belözoglu were previously team-mates at Fenerbahce, sharing the dressing room during the period that culminated in the club's 2014 league title.
Belözoglu now returns in a different capacity, with the immediate task of preparing the team for Liverpool and establishing his own direction at the club.