Match report: PNE 1 Fulham 2
The Serbia international, on loan from Newcastle United, scored both of the Cottagers' goals - the winner in stoppage-time - to give them a barley-deserved victory.
Mitrovic has now scored six goals against North End in four appearances over the last 18 months.
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Hide AdHe had opened the scoring in the 69th minute but PNE deservedly levelled seven minutes later through another Sean Maguire goal.
The Irishman headed home his fourth goal in three games, the ball slipping through the gloves of Marcus Bettinelli.
North End looked on course for a point until Mitrovic headed home a Tom Cairney cross in the 91st minute.
The North End side had shown two changes from the one which won 2-1 against Bristol City last Tuesday, Maguire and Daniel Johnson starting in place of Billy Bodin and Paul Gallagher respectively.
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Hide AdThere was a return on the bench for skipper Tom Clarke after a month out with injury but Louis Moult missed out through illness.
PNE's high pressing game saw them have the better of the early play and carve out a couple of decent chances.
Callum Robinson's low shot forced Bettinelli into a diving save in the fourth minute after Ben Pearson and Maguire had worked the ball across the face of the box.
Right-back Darnell Fisher worked Bettinelli again when he connected with Robinson's scooped pass, his shot from the right side of the box pushed round the near post by the keeper.
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Hide AdThe visitors' first sight of goal came in the 20th minute when Stefan Johansen get away down the left channel, Greg Cunningham and Pearson combining to clear the danger.
As Fulham began to find their rhythm going forward, Matt Targett tested Declan Rudd with a low shot from 20 yards which the Preston keeper got behind to save.
Ryan Fredericks' low cross from the right was missed by Ryan Sessegnon sliding in at the far post, then Rudd got down well to save Mitrovic's low shot from the left hand side of the box.
Four minutes before half-time, Maguire got behind the Fulham defence as he chased a Rudd goalkick.
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Hide AdHe made room for himself in the box but Bettinelli and the covering Denis Odoi combined to block his shot.
At the interval Cunningham was replaced by Calum Woods, Cunningham looking like he had struggling with an injury late in the first half.
Rudd made a superb save in the 48th minute, diving to his left to tip a 20-yards shot from Floyd Ayite over the bar.
Just beyond the hour, Pearson's pass sent Barkhuizen away, the winger cutting into the box but getting crowded out by two defenders as he shaped to shoot.
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Hide AdThe clash went up another level when Fulham took the lead in the 69th minute.
Substitute Cyrus Christie chased a pass down the Cottagers' right channel, hurdling a sliding challenge from Woods, before pulling the ball back into the middle for Mitrovic to slam home a first-time shot.
North End almost pulled level within six minutes when a Robinson corner dropped deep beyond the back post.
Alan Browne hooked it back into the path of Ben Davies, his low shot palmed out of the six-yard box by Bettinelli and cleared
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Hide AdWithin a minute though, they got the equaliser their play deserved.
Pearson got the ball on the right and chipped a cross into the middle which Maguire met with a downward header.
The keeper seemed to have it covered but it slipped through his gloves and into the net, that sending Deepdale wild.
North End pressed for a second goal but it was Fulham who found the net a minute into stoppage-time to stun the stadium into silence - bar the 968 travelling fans.
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Hide AdFisher switched off when defending a throw-in on the visitors' left flank, Cairney getting space to lift a cross over to the far post where Mitrovic rose to send a header back across Rudd into the net - it almost happening in slow-motion.
PNE: Rudd, Fisher, Huntington, Davies, Cunningham (Woods 46), Pearson, Johnson (Harrop 83), Robinson, Browne, Barkhuizen, Maguire (Bodin 83). Subs (not used): Clarke, Horgan, Gallagher, Maxwell.
Fulham: Bettinelli, Fredericks (Christie 67), Odoi, Ream, Targett, McDonald, Johansen, Ayite (Piazon 59), Cairney, Sessegnon (Ojo 83), Mitrovic. Subs (not used): Fonte, Norwood, Kamara, Button.
Referee: Simon Hooper (Wiltshire)
Attendance: 12,970 (968 away)