The third came shortly before the break when Ryan Shawcross headed in Wilson's flick from Jermaine Pennant's corner.
His corner presented Ryan Shawcross with a free header, which Paul Robinson kept out with a brilliant one-handed save.
The Arsenal star had surgery after fracturing the fibula and tibia in a challenge with Stoke City's Ryan Shawcross last weekend.
Blackburn doubled their lead after 18 minutes, Roberts scrambling home from close range after Brett Emerton's cross rebounded into his path off Ryan Shawcross.
But with three minutes remaining James Beattie crossed for Ryan Shawcross to head in and, at the death, Whelan's fierce drive earned Stoke a point.
Stoke almost ruined their vaguely promising start when Ryan Shawcross made a rash challenge on Malouda in the box and referee Martin Atkinson awarded a penalty.
Wenger also revealed that midfielder Aaron Ramsey was showing good progress in his recovery from a double broken leg suffered in a tackle with Stoke's Ryan Shawcross.
Ramsey, who was injured in a tackle by Stoke's Ryan Shawcross started his first game for Arsenal last weekend after loan spells at Nottingham Forest and Cardiff.
The contest was back on and the visitors sensed a miraculous recovery but Ryan Shawcross spurned a good chance as he headed tamely into the hands of Marcus Hahnemann.
Ramsey signed a new long-term Arsenal deal in June 2010 - a boost after he suffered a double leg break following a tackle by Stoke City defender Ryan Shawcross in February.
Firstly, Danny Pugh came on for Andy Wilkinson, then Ibrahima Sonko for Ryan Shawcross and, finally, Ricardo Fuller was replaced by debutant Henri Camara after falling awkwardly and damaging his shoulder.
Pulis believes he has a good knowledge of players and signed the likes of Ryan Shawcross and Richard Cresswell during the summer, while Danny Pugh and Leon Cort arrived on loan early in the season.
But Stoke improved as the half wore on and went close when Robert Huth's free kick found its way through to Ryan Shawcross and the centre-half's shot on the turn was blocked by two Wigan defenders.
The home supporters then thought they should have had a penalty when Stoke defender Ryan Shawcross tangled with Julien Faubert in the box, but referee Howard Webb decided the English defender had timed his tackle well.
And both Rooney and Milner said Stoke defender Ryan Shawcross, who is in an England squad for the first time and whose challenge on Aaron Ramsey at the weekend resulted in a double compound fracture for the Arsenal midfielder, had been made welcome.
Hull had committed unnecessary numbers forward and were holding a worryingly high a line at the back when Mendy inexplicably missed a Ryan Shawcross punt upfield, allowing Ethrington to race in from the left and lash a powerful near-post finish past Matt Duke.
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