Lewis Guy scored as Doncaster reached the FA Cup second round and increased Brentford's winless run to 15 games.
Guy scored with a low drive after skipping round three tackles just a minute after Bees new boy Fola Onibuje had headed over from just six yards.
Ex-Bees Jason Price and Mark McCammon could also have scored for Rovers.
Jo Kuffour shot just over for Brentford but they left the field to a chorus of boos and with fans calling for the dismissal of manager Leroy Rosenior.
Brentford: Masters, O'Connor, Frampton, Griffiths, Tillen, Brooker, Skulason (Pinault 46), Mousinho, Kuffour, Onibuje (Moore 60), Ide (Wijnhard 74).
Subs Not Used: Brown, Tomlin.
Booked: Brooker, O'Connor, Moore.
Doncaster: Smith, O'Connor, Stephen Roberts, Lockwood, Gareth Roberts, Price, Stock, Paul Green, Guy (Streete 90), McCammon (Thornton 89), Forte (Heffernan 85).
Subs Not Used: Griffith, Richardson.
Goals: Guy 32.
Ref: D Whitestone (Northamptonshire).