Rovers under-17s hosted Athlone Town at The Showgrounds for their final home game of the inaugural season of the league.
Athlone took a 1-0 lead into the second half but early in the second half Thierry Baba was taken down in the penalty area and Liam Kerrigan scored from the spot.
The visitors went in front again with 15 minutes to go but within 10 minutes Darren Somers scored his first for the club to level the game again.
But in stoppage time Athlone went ahead for the third time and there was no chance for Rovers to make another comeback.
Sligo Rovers team: Callaghan, Benson, Mahon, Smith, McDermott, McGarry, Feeney, Kerrigan, Mullarkey, Hever, Byrne.