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At least no one can accuse Arsène Wenger of devaluing the FA Cup any more. Arsenal’s desperation for silverware produced a magnificent cup-tie that they won deservedly in controversial fashion, but their valiant comeback was soon forgotten as a result of the shenanigans that followed it.

Spitting allegations and tunnel bust-ups competed with claims that Hull City were cheated by the referee for attention in a remarkable postscript that is likely to run for a good while yet. All that was missing from a night of frenzied acrimony was a flying pizza, although Cesc Fàbregas, said to be the thrower of the most famous piece of pepperoni slice in footballing history, somehow managed to get in on the act despite sitting out the match because of injury.

After the dust has settled — which will take several days and is likely to require some involvement from the FA — all that really matters is that Fàbregas and his team-mates can look forward to an FA Cup semi-final against Chelsea next month, and with it the prospect of ending their four-year wait for silverware.

For all Hull’s character and chutzpah in attempting to pull off a second win of the season at the Emirates this was the right result because Arsenal laid siege to the visiting team’s goal during the second half and their own goalkeeper, Lukasz Fabianski, was a virtual spectator. Geovanni hit the side-netting as he sought to emulate his remarkable winner here in September, but otherwise Hull were on the back foot.

Arsenal were worthy victors, but the nature of their winner left a sour taste, which may go some way to explaining Phil Brown’s extraordinary post-match claims, which could prove impossible to verify. William Gallas was offside when Boaz Myhill came and missed Samir Nasri’s free kick in the 84th minute and the goal should not have stood despite Wenger’s claims to the contrary. The Hull goalkeeper did get a touch of the ball, but not before Johan Djourou, thereby putting Gallas in an offside position. Wenger’s version of justice is distinctly one-eyed.

It says a great deal about Hull’s tenacity — and their own desperation for success — that everyone associated with Arsenal celebrated Gallas’s winner as if it had brought them the European Cup itself. Even with thousands of empty seats in a crowd that looked far smaller than the official attendance of 55,641 this stadium has hardly witnessed such a wild roar.

For a long time such an outpouring of joy did not look like coming, as Hull seemed intent on proving that lightning can indeed strike twice, much to the delight of their impressive travelling support. Many of those fans will have already witnessed something that they never thought possible when Hull won at the Emirates in September, yet still came back for more.

This combination of blind faith and utter devotion looked like being rewarded as Hull dominated the first half. Andy Dawson’s speculative pass down the left caught Gallas unawares and found its way to Nicky Barmby, who lifted the ball over Fabianski into the net with the aid of a deflection off Djourou.

The 35-year-old celebrated as if he had scored the goal of the season, although in the circumstances such emotion was understandable, because he has reached the stage in his career when every goal could be his last.

Hull were not finished, however, and with an extra man giving them control of midfield they pushed on for a second which, with greater fortune, could have come their way before half-time. Geovanni came close to adding another stunner to the winner he scored here earlier in the season, but his free kick in the 23rd minute was tipped round the post by Fabianski and, from the resulting corner, Barmby poked the ball in to the net from another cross by Dawson, only correctly to be ruled offside.

Arsenal’s only real attacking threat in the opening 45 minutes came courtesy of Theo Walcott’s pace down the right, but from the start of the second half they demonstrated greater potency. In the space of two minutes, Arsenal created enough opportunities to have won the game, with Abou Diaby heading wide from a corner, Andrey Arshavin shooting into a crowded penalty area and Robin van Persie having a header blocked before Alex Song shot across the face of goal.

Arshavin seemed to offer Arsenal’s best hope of a breakthrough and the Russian was involved in their equaliser in the 74th minute, squaring the ball to Van Persie after being played in by Nicklas Bendtner, a substitute.

While Van Persie’s goal was richly deserved, it was difficult not to feel sorry for Brown’s battlers after Gallas’s late winner, which brought an abrupt end to the prospect of Hull’s biggest day out since the entire city travelled to Wembley for the Hull KR v Hull Rugby League Challenge Cup final in 1980. Instead, Arsenal will meet Chelsea at the national stadium in an altogether more metropolitan derby, which will do well to produce as much drama as this feisty encounter.

Arsenal (4-4-2): L Fabianski — B Sagna, W Gallas, J Djourou, K Gibbs — T Walcott (sub: E Eboué, 82min), A Diaby, A Song (sub: S Nasri, 65), A Arshavin — R van Persie, C Vela (sub:N Bendtner, 65). Substitutes not used: V Mannone, K Touré, Denilson, M Silvestre. Booked: Gallas, Nasri.

Hull City (4-5-1): B Myhill — S Ricketts, K Zayatte, A Gardner, A Dawson — C Fagan, N Barmby (sub: R France, 76), I Ashbee (sub: B Hughes, 46), Geovanni, P Halmosi (sub: B Mendy, 68) — Manucho. Substitutes not used: M Duke, R Garcia, C Folan, N Featherstone. Booked: Halmosi, Myhill, Dawson, France, Manucho, Geovanni.

Referee: M Riley.