The 24-year-old scored his eighth goal in 29 league appearances to put the Stade de l'Aube’s outfit in front but Robert Beric’s second-half brace secured the three points for the hosts.
The former Nantes player open the scoring with eight minutes into the encounter. But Jean-Louis Gasset’s men launched a powerful comeback in the second-half with a 68th-minute goal from Beric.
The Slovenia international then completed his brace five minutes later as the Greens added more woes to their opponents who have now lost four consecutive games.
Niane featured for 65 minutes before making way for Gabonese midfielder Johann Obiang.
The defeat has further dented Troyes’ hope of avoiding the drop at the end of the season after managing 29 points from 34 games.
They will be looking to return to winning ways when they take on Caen in their next league game on April 28.