Winger Volkan Şen scored the first goal of the game just three minutes in.
The home side dominated the first half but both sides failed to score another goal.
Beşiktaş was a little more offensive in the second half mainly thanks to attacking midfielder Gökhan Töre, who came in for Olcay Şahan.
However, Fener remained dangerous with counterattacks, and its Portuguese midfielder Luis Nani, the former Manchester United star, struck a second goal in the 82nd minute, sealing the crucial win.
“I am glad that we had a deserved win,” said Fener coach Vitor Pereira in a post-game interview.
“I felt that we are a team. I will have a good sleep tonight,” he said, noting that his side is the sole Turkish team remaining in the UEFA Europa League.
Fener was drawn against Portuguese club Braga in the last 16 of the UEFA Europa League Round. The last 16 matches will be played on March 10 and 17.
“As the team keeps winning, it is not important for me if I am substituted,” said Nani.
“My players gave all that they could,” said a disappointed Beşiktaş coach Şenol Güneş after the game. “We are a good team and I think we will reclaim top spot and clinch the title.”
Fenerbahçe now leads the standings with 53 points, two points more than Beşiktaş, which still has a game in hand.
Third-placed Torku Konyaspor has 40 points. Medipol Başakşehir and Galatasaray round out the top five with 39 and 37 points, respectively.
Galatasaray, which lost 2-0 against Gaziantepspor over the weekend and is now 16 points behind Fener, produced confusion amid media reports that said coach Mustafa Denizli had resigned only for chairman Dursun Özbek to refute them.
Denizli was due to resign from last year's champions on Feb. 29 after a three-month spell with the club, Reuters quoted a source close to the matter as saying.
Denizli took charge at the club in November 2015 after former coach Hamza Hamzaoğlu stayed less than a year at the helm.
Denizli, 66, managed the Turkish national team for four years and reached the quarter-finals of Euro 2000.
He has won three domestic league titles with Istanbul's three arch-rivals – Galatasaray, Fenerbahçe and Beşiktaş.