Following on from a disappointing midweek 1-1 draw with St Monans Swallows, where a late late goal from Brown had ensured a share of the points, Thistle moved on to a Wallace Wright Cup tie.
Thistle had a chance to take the lead on the quarter hour when Jukes released Shepherd who was crudely sent tumbling in the box by Anderson resulting in a penalty.
Barnes stepped up but his poor spot kick was easily saved by Strathearn.
Thistle were struggling to get going with the hosts having the upper hand and it came as no surprise when they took the lead just before the half hour when a poor clearance from McArthur was collected by Hughes who slammed the ball home.
Thistle made a couple of changes at the break with Ross and Band making way for Gorgon and McLaren and it was Gorgon who brought his side back level in the tie on the 55th minute when he headed home a long throw from Brown.
The match seemed to be destined for penalties until a moment of madness from Henderson gifted Rosyth the winner in the final minute.
The keeper had gathered a Bowman shot, but opted to try and instantly send the ball up field and instead only managed to send his kick off the back of Hughes.
With the ball heading towards the net Moir reacted to try and clear the danger, but appeared to be impeded by Hughes as the ball rolled into the net. The referee adjudged the challenge was fair allowing the goal.
Further misery ensued for Thistle with Moir and McArthur failing to control their discipline and getting sent off for their protests.
Alba Mortgage Solutions Man of the Match – Liam Carson.
Thistle – Henderson, Ireland (Petrie 57), Ross (Gorgon 46), Carson, Brown, Shepherd, McArthur, Band (McLaren 46), Moir, Barnes (McShane 68), Jukes
Sub – C Murray.