Arsenal struck first with a typically incisive move that ended with Andrey Arshavin firing in from close range.
Sol Campbell's foul on what looked an offside Jan Vennegoor of Hesselink allowed Jimmy Bullard to fire Hull level from the penalty spot.
Hull battled well after George Boateng was sent off but Bendtner fired home in injury time to give Arsenal victory.
This was not a vintage performance from the Gunners but that will be of no concern to boss Arsene Wenger, whose side are now second in the table and only behind Chelsea on goal difference.
But for Hull a cruel defeat means they remain three points behind West Ham and Wolves who are tied on 27 points in 16th and 17th place in the league respectively.
While both Arsenal and Hull have more pressing current league concerns at the top and bottom of the table, it was almost inevitable that this game would contain moments of controversy.
The teams were fined for a mass brawl when they met in December, while Arsenal captain Cesc Fabregas was cleared of spitting after last season's FA Cup clash, while Hull boss Phil brown, who made the Fabregas allegation, was fined £2,500 over comments in relation to referee Mike Riley.
On this occasion, chief among the talking points emerging from this match was the dismissal of Boateng, courtesy of two bookings within a five-minute spell at the end of the first half.
The midfielder was firstly carded, along with Arsenal striker Bendtner for an off-the-ball clash between the two.
While his first booking was for a needless exchange his second arrived for a shockingly high tackle on Bacary Sagna and the only debating point could be whether the challenge should have warranted a straight red.
It was a sad end to what had been an engrossing 45 minutes of football that featured two contrasting sides and two contrasting goals.
Arsenal struck first in the 14th minute when Bendtner found Arshavin on the edge of the box and he jinked his way past two Hull players, one being Bernard Mendy, whose inadvertent flick set the ball up perfectly for the Russian to fire past keeper Boaz Myhill.
It was Arsenal's 100th goal of season and their 800th in the Premier League, but they were not ahead for long.
The scorer of Hull's equaliser, Bullard, was himself embroiled in a controversial incident this week.
On Monday, he was involved in a public fracas with team-mate Nicky Barmby but when called upon to demonstrate his professionalism he made no error with a well-taken if not contentiously awarded penalty.
Vennegoor of Hesselink looked offside when Dean Marney's looping ball fell into his path in the box but referee Andre Marriner waved play on just before the striker was bundled to the ground by Campbell.
It was debatably a goal scoring opportunity with Campbell the last man but the centre-back stayed on the pitch to witness Bullard fire his spot kick into the roof of the net.
After a low-key start to the second half, during which Arsenal failed to make inroads into their numerically inferior opponents, they introduced Theo Walcott.
The winger almost made an immediate impact, bursting down the right before producing a cross that found its way to Arshavin via a touch from Samir Nasri, but the Russian ballooned his shot over.
Danish striker Bendtner has had a rollercoaster week in an Arsenal shirt having come in for heavy criticism for the chances he missed in last Saturday's league fixture with Burnley before being lauded for his hat-trick display in Tuesday's Champions League tie against Porto.
And the second half at Hull again highlighted the hit and miss nature of his game as he missed two presentable chances before providing the match-winner two minutes into injury time.
Denilson's speculative long-range effort arrived straight at Myhill, but the keeper merely palmed it straight to Bendtner who made no mistake in firing Arsenal's seventh injury-time winner of the season.
