Marc Nygaard put Rangers in front early in the game when he fired the ball past keeper Steve Simonsen from 10 yards.
Hoefkens equalised with a penalty after Darel Russell was fouled by Danny Shittu, before Sigurdsson's winner.
Gareth Ainsworth had a penalty saved by Simonsen with the scores at 1-0, after Dave Brammer fouled Lee Cook inside the 18-yard area.
QPR caretaker manager Gary Waddock:
"We could have been at 2-0. The penalty changed the game.
"It's deflating, but we really need to be more clinical in front of goal. We need to take our chances."
QPR: Jones, Bignot, Shittu, Evatt, Milanese, Ainsworth (Furlong 80), Bircham (Langley 78), Lomas, Cook, Youssouf (Moore 15), Nygaard.
Subs Not Used: Cole, Santos.
Goals: Nygaard 7.
Stoke: Simonsen, Hoefkens, Duberry, Wilkinson, Broomes, Chadwick (Buxton 88), Brammer, Russell, Sweeney (Gallagher 71), Bangoura (Sidibe 71), Sigurdsson.
Subs Not Used: de Goey, Mbuyi.
Booked: Bangoura, Wilkinson.
Goals: Hoefkens 73 pen, Sigurdsson 79.
Ref: P Walton (Northamptonshire).