The Portuguese former Manchester United, Chelsea and Real Madrid manager told reporters he believed his striker Edin Dzeko was onside, and displayed a frame from the build-up to the strike to prove his point.
"For us, it's a good goal," Mourinho said after the 2-0 win at Antalyaspor in the Turkish Super Lig.
"I like good VAR... I just want a VAR that helps the referee to take the right decisions."
Fenerbahce chairman Ali Koc had accused Turkish Super Lig's video assistant referees of bias against his club last April, with the league deciding to hire foreign VARs for the rest of the 2023-24 season.
Last season's runners-up Fenerbahce are second in the table with 16 points from seven matches, three points behind champions Galatasaray. Mourinho's side will visit FC Twente in the Europa League on Thursday.