A spirited Tranmere performance was undone by a minute of madness that saw Rovers concede twice in sixty seconds to go out of the Carling Cup.
Rovers led at half time through Enoch Showunmi, but quick-fire goals from Van Der Gun and sub Scott Sinclair put Swansea ahead, before Kuqi fired home on the counter attack in injury time.
The scoreline was an unfair reflection on a game that saw Tranmere comfortably keep their Championship opponents at bay for 75 minutes of the game.
Parry made only one change to the side that started against Bournemouth, with Max Blanchard coming in for Nick Wood.
Ian Goodison was passed fit despite an ankle injury, while John Welsh was given the captaincy with Ian Thomas-Moore's transfer situation dragging on.
The first half display was full of the vim and vigour that categorised last season's displays against bigger clubs, and Rovers had already gone close through Joss Labadie when they went on to take the lead after 20 minutes.
A long ball from goalkeeper Collister saw the Swans' centre half and keeper hesitate, and Showunmi nipped in to head round De Vries and find the net from a tight angle.
From that point on Rovers created little, but new captain John Welsh and Labadie buzzed around the centre of the park and made things difficult for the Welsh side.
Thomas-Moore and Gornell were muted as an attacking threat as the Swans kept possession and forced them deeper, but at half-time Rovers had held firm without really looking like conceding.
Rovers got an early let-off in the second half when Joe Collister showed just why his manager believes he has a big future with a tremendous save from Allen from inside the box, throwing up a strong right hand to deny the Swans an equaliser.
Other than that scare though, Rovers looked content to sit on their lead, and dealt well with Swansea's early attempts to break them down.
In fact, it was only after manager Brendan Rogers threw on former Chelsea winger Sinclair in the 60th minute that Swansea really began to threaten.
Critics will suggest that Parry should have responded to the change with one of his own, but there was little his side could do about the freakish nature of the equaliser.
A shot from the edge of the area by Orlandi came back off the crossbar, and with Collister unsure of where the ball was, hit Van Der Gun before trickling past Goodison's outstretched leg.
What will disappoint the Rovers boss is his team's reaction to going a goal down.
As on Saturday, heads dropped, and within seconds it was two.
Scott Sinclair showed just why he was so highly rated at Chelsea, as he twisted past two challenges, accelerated away from Darville and slotted calmly past Collister.
But despite the class of the finish, it all looked too easy for the young winger.
Parry responded to the goals with a double change, bringing on new signings McGurk and Akins and switching to 4-4-2.
There was little to threaten the Swansea goal though, as a tired Rovers simply went through the motions, the turnaround from winning to losing having knocked the stuffing out of them.
The third goal came as Kuqi caught Rovers on the break, racing clear of Cresswell before beating Collister at his near post.
Rovers now travel to Dagenham & Redbridge at the weekend, where they will be looking to build on two impressive away results last week.
But after three defeats in three at home, Parry has a lot to think about before the visit of Peterborough next Saturday.
Rovers side: Collister, Darville, Blanchard, Goodison, Cresswell, Labadie, McLaren (McGurk 82), Welsh, Thomas-Moore, Showunmi, Gornell (Akins 82)
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