It started well for Rovers with Jack Hever scoring first after just five minutes.
But a penalty 10 minutes later to Athlone got them level. A second penalty was given just before half-time but keeper Luke McNicholas saved.
The game reamined level until the final 20 minutes when two quick goals for the home side gave them the win.
Niall Harrison's side will be back at The Showgrounds on Saturday. Salthill Devon are the visitors and the game kick off at 1pm.
Team: Luke McNicholas, Thierry Baba, Jack Hever, Ryan Smith, John Mahon, Jack Mullarkey, Ruadhan Feeney (c), James McGrath, Liam Kerrigan, Gary Higgins, Mark Byrne.
Subs: Niall Morahan, Michael McGarry, Jordan Muldoon, Darren Somers, Conor Burke, Lorcan Callaghan.