Visitors Konyaspor's Kosovan winger Zymer Bytyqi scored from close range in the minute 35, following a rebound by Fenerbahce goalkeeper Altay Bayindir.
Fenerbahce players argued with the referee that Bytyqi fouled the goalie before his finishing touch, while the referee said the goal was valid.
Konyaspor led the first half at Istanbul's Ulker Stadium.
In minute 66, Fenerbahce's South Korean defender Kim Min-jae scored an easy chance to level the match.
Fenerbahce midfielder Irfan Can Kahveci whipped a freekick as Konyaspor goalkeeper Ibrahim Sehic plunged to parry it. However, the ball hit the bar and was on the loose then. Kim was in the right place to score an open goal.
In the 88th minute, Fenerbahce completed the 2-1 comeback.
Home team's Greek midfielder Dimitris Pelkas scored a classy goal in the box as the winning goal for Fenerbahce.
Fenerbahce boosted their points to 53 in 30 matches to be in third position in the league table.
They narrowed the gap against second-place Konyaspor, who have 55 points.
Trabzonspor are getting closer to winning the 2022 Super Lig title.
The Black Sea club collected 70 points in the 2021-22 Super Lig season that will end in eight weeks.
GALATASARAY STUNNED BY GAZİANTEP TO UPSET FANS
Recently eliminated by Barcelona in the UEFA Europa League, Galatasaray were on Sunday stunned by Gaziantep FK 3-1 to go on to frustrate their fans.
In the 34th minute, Galatasaray's French forward Bafetimbi Gomis scored the opening goal in Gaziantep's Kalyon Stadium.
But the Istanbul team were unable to secure the 1-0 lead as Senegalese defender Papy Djilobodji scored the equalizer near the end of the first half.
Gaziantep FK were awarded a penalty in the second half when Berkan Kutlu fouled Joao Figueiredo in the area.
In minute 71, Romanian midfielder Alexandru Maxim scored from the white spot as Gaziantep FK came back.
Figueiredo scored the third goal for Gaziantep FK in the 81st minute after Maxim's solo and industrious effort in the area.
In the second half, Gomis missed a couple of chances. So Galatasaray returned home with a 3-1 loss.
Gaziantep FK are in the 12th spot with 40 points.
Meanwhile Galatasaray, who are spending a terrible season in the domestic league, bagged 38 points in 30 matches to rank 15th.
The Lions are close to the league's relegation zone.
After the next week's international break for the 2022 FIFA World Cup qualifiers, the Turkish Super Lig will continue to be played on April 2.
RESULTS:
Caykur Rizespor - Trabzonspor: 3-2
VavaCars Fatih Karagumruk - Yukatel Kayserispor: 3-0
Oznur Kablo Yeni Malatyaspor - Kasimpasa: 0-2
Goztepe - Aytemiz Alanyaspor: 0-2
Adana Demirspor - Medipol Basaksehir: 2-1
Besiktas - Atakas Hatayspor: 1-1
Fraport TAV Antalyaspor - GZT Giresunspor: 4-1
Demir Grup Sivasspor - Altay: 2-1
Gaziantep FK - Galatasaray: 3-1
Fenerbahce - Ittifak Holding Konyaspor: 2-1
- League table
| Clubs | P | W | D | L | GF | GA | +/- | Pts |
| 1. TRABZONSPOR | 30 | 21 | 7 | 2 | 58 | 26 | 32 | 70 |
| 2. ITTIFAK HOLDING KONYASPOR | 30 | 16 | 7 | 7 | 48 | 33 | 15 | 55 |
| 3. FENERBAHCE | 30 | 15 | 8 | 7 | 50 | 35 | 15 | 53 |
| 4. AYTEMIZ ALANYASPOR | 30 | 14 | 7 | 9 | 55 | 47 | 8 | 49 |
| 5. ADANA DEMIRSPOR | 30 | 13 | 9 | 8 | 46 | 32 | 14 | 48 |
| 6. MEDIPOL BASAKSEHIR | 30 | 14 | 5 | 11 | 42 | 31 | 11 | 47 |
| 7. ATAKAS HATAYSPOR | 30 | 14 | 5 | 11 | 48 | 46 | 2 | 47 |
| 8. BESIKTAS | 30 | 12 | 10 | 8 | 44 | 39 | 5 | 46 |
| 9. VAVACARS FATIH KARAGUMRUK | 30 | 12 | 7 | 11 | 36 | 43 | -7 | 43 |
| 10. FRAPORT TAV ANTALYASPOR | 30 | 11 | 8 | 11 | 34 | 36 | -2 | 41 |
| 11. DEMIR GRUP SIVASSPOR | 30 | 10 | 10 | 10 | 40 | 38 | 2 | 40 |
| 12. GAZIANTEP FK | 30 | 11 | 7 | 12 | 40 | 42 | -2 | 40 |
| 13. KASIMPASA | 30 | 10 | 8 | 12 | 45 | 43 | 2 | 38 |
| 14. YUKATEL KAYSERISPOR | 30 | 10 | 8 | 12 | 43 | 48 | -5 | 38 |
| 15. GALATASARAY | 30 | 10 | 8 | 12 | 40 | 45 | -5 | 38 |
| 16. GZT GIRESUNSPOR | 30 | 10 | 5 | 15 | 32 | 37 | -5 | 35 |
| 17. ALTAY | 30 | 8 | 5 | 17 | 31 | 43 | -12 | 29 |
| 18. GOZTEPE | 30 | 7 | 6 | 17 | 36 | 50 | -14 | 27 |
| 19. CAYKUR RIZESPOR | 30 | 7 | 5 | 18 | 29 | 55 | -26 | 26 |
| 20. OZNUR KABLO YENI MALATYASPOR | 30 | 5 | 5 | 20 | 23 | 51 | -28 | 20 |
