The Tigers went ahead on Nicky Barmby's early strike and held off Arsenal until Van Persie equalized from inside the penalty area with 16 minutes left.
Gallas set up the semifinal date against his old club when he scored from close range, though replays showed the Frenchman was clearly offside. Arsenal manager Arsene Wenger insisted Samir Nasri's free kick had been first fisted by American-born keeper Boaz Myhill before it fell to Gallas.
After the match Hull manager Phil Brown accused Arsenal's Cesc Fabregas, who is sidelined, of spitting at assistant boss Brian Horton in the tunnel after the game. The Spaniard denied the charge.