Besiktas scored the opener in the minute 29 as Cameroonian forward Vincent Aboubakar's header beat Trabzonspor goalkeeper Ugurcan Cakir at the Vodafone Park in Istanbul.
This was Aboubakar's 12th league goal in the 2020-21 season.
Near the end of the first half, Trabzonspor found a lucky goal as Nwakaeme's shot was deflected twice to beat Besiktas goalie, as the own goal credits went to defender Francisco Montero.
In the minute 63, Brazilian defender Vitor Hugo scored with a right footed strike in the area to bring 2-1 lead for the visitors, completing the comeback.
In the 77th minute, Besiktas were down to ten men on the pitch as Turkish midfielder Dorukhan Tokoz was shown the red card for a harsh tackle against his opponent.
Besiktas took risks, preferring an ultra-attacking play to create chances.
But Trabzonspor defended well to secure the 2-1 victory in Istanbul.
'Big Three' rule top positions
The Super Lig's "Big Three" are now dominating the division's top spots this season.
League leaders Fenerbahce have 45 points. Second-place Besiktas are chasing them with 44 points.
Galatasaray are currently in the third spot as the Lions so far bagged 42 points. Sunday's victors Trabzonspor moved to the fifth position in standings as the Black Sea team boosted their points to 36.
Trabzonspor are following fourth-place Aytemiz Alanyaspor, as they have 37 points.
Results of week 22:
Yeni Malatyaspor - Fatih Karagumruk: 0-0
Gaziantep FK - Galatasaray: 1-2
Kasimpasa - Hes Kablo Kayserispor: 0-1
Medipol Basaksehir - Atakas Hatayspor: 1-5
Fenerbahce - Caykur Rizespor: 1-0
Aytemiz Alanyaspor - Demir Grup Sivasspor: 3-1
Buyuksehir Belediye Erzurumspor - MKE Ankaragucu: 1-0
Yukatel Denizlispor - Goztepe: 2-1
Genclerbirligi - Fraport TAV Antalyaspor: 0-1
Besiktas - Trabzonspor: 1-2
