Ankaragucu from the Turkish capital leveled the score in minute 26 when Ibrahim Akdag successfully converted a penalty shot.
Two minutes later, Ekuban scored again to put his team in front for good, finishing at close range after displaying individual skill.
In the 30th minute, Trabzonspor's Djaniny quickly dribbled into the box after winning the ball in the midfield area and passed Ankaragucu goalkeeper Ricardo Friedrich to put the ball into Ankaragucu's net.
That goal made things easier for Trabzonspor.
In minute 38, Friedrich was injured and the Brazilian was replaced by Korcan Celikay.
In the 94th minute, Trabzonspor's Edgar made it 4-1.
Yusuf Sari took a freekick. Celikay parried it but Edgar got to the rebound and scored from close range.
Trabzonspor secured the win after being beaten by Aytemiz Alanyaspor 3-1 and then drawing with Buyuksehir Belediye Erzurumspor 0-0 last weekend.
Fourth-place Trabzonspor have 55 points in 30 matches. They are closely following Fenerbahce, who have had 58 points in 29 games.
Ankaragucu are now in the 17th position with 29 points. The Ankara team are feeling the heat of the relegation zone.
Sivasspor win 8-goal thriller
Demir Grup Sivasspor beat Goztepe 5-3 in an away match in this weekend's surprising result.
Sivasspor had a 5-0 lead for an hour as forward Mustapha Yatabare and winger Tyler Boyd each scored twice. Sivasspor's Faycal Fajr had a goal on a classy shot outside the area in Izmir's Gursel Aksel Stadium.
The 5-0 lead of the visitors stunned Goztepe.
Goztepe came alive with three goals in the last 30 minutes of the clash when forward Cherif Ndiaye, defender Titi and winger Fousseni Diabate scored for the Izmir club.
But the late heroics fell short as Sivasspor clinched the victory.
Genclerbirligi - Kasimpasa: 2-1
Goztepe - Demir Grup Sivasspor: 3-5
Yeni Malatyaspor - Gaziantep: 2-2
Trabzonspor - MKE Ankaragucu: 4-1