The former Real Madrid star’s deal was not due to expire until June 2019, but Besiktas have been left with no choice but to terminate his deal as a result of ongoing financial issues.
The club released a statement confirming Pepe’s departure and thanking him for his efforts on Monday.
It has been reported that Pepe left a cash tip for several staff members who have worked alongside him in recent years.
The centre-back is said to have been one of the highest earners in the Besiktas squad after signing a two-year deal with the Turkish side following the expiration of his Real Madrid contract in 2017.
The deal was apparently worth €9.5 million (£9m/$11m) before bonuses and it has also been claimed that Pepe received a hefty bonus after every match he participated in.
He has left the club on good terms and said farewell when he attended their 2-2 draw with Trabzonspor at the Vodafone Park Stadium on Sunday.
Despite a number of niggling injury issues, Pepe had made 17 appearances for the club this season and registered an impressive five goals. He was a mainstay of Senol Gunes’ backline and is still one of Portugal's first choice centre-backs.
It remains to be seen where the veteran defender will look to continue his career, with some reports suggesting that he may look to return to Portugal.
Alvaro Negredo has had to leave the club for similar reasons and joined Al-Nasri in September, whilst forward Ryan Babel has also been told that he will need to look for a new team when his contract expires next year.