Belfast's Frampton, 29, was in full control of the first half of the fight, during which his opponent simply could not find his range.
Bury's Quigg, 27, finally came alive down the stretch as the contest turned into a desperate tussle, but Frampton gave as good as he got.
Bizarrely, one judge scored it 115-113 for Quigg, while the two others scored it 116-112 in Frampton's favour.
Frampton said: "The travelling support has been unbelievable - this isn't Manchester, is it? Seems like it is Belfast.
"I couldn't believe it was a spilt [decision]. I don't know what that lad was watching. He needs to take a long hard look at himself.
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"I knew it was going to be a boring fight - I had to sell it for TV. I knew I had the brain to do that and make it boring."
Although there was no rematch clause in the contract, there was a verbal agreement that they would do it all again in Belfast if the first fight warranted it.
And while it was a slow-burner, a cracking second half ensued, which sent the 20,000 fans packed into the Manchester Arena into raptures - and will surely mean a return will take place later this year.
It was Quigg's first defeat in 34 professional fights, stretching back to 2007. Frampton is undefeated in 22 fights since turning pro in 2009.
Frampton-Quigg was one of the most eagerly-anticipated domestic match-ups in recent memory, and the first time two undefeated British boxers had fought to unify a world title.
The Northern Irishman was a narrow favourite with the bookmakers. However, his odds lengthened after he was knocked down twice by unheralded Mexican Alejandro Gonzalez last July, on the same day that Englishman Quigg demolished tough Spaniard Kiko Martinez - who had taken Frampton the distance in 2014.
Both men claimed to have won the mind games during a heated build-up, as well as insisting they were the better boxer and that losing was not an option.
While it was expected there would be an even split of fans, the reactions to the fighters' entrances suggested Frampton had the lion's share of support, despite Quigg being the 'home' fighter.
Frampton probably nicked a largely non-eventful first round courtesy of a couple of crisp jabs, while the second went largely the same way until the last minute, when Quigg finally came out of his shell.
There was more engagement in the third, with Frampton continuing to stalk his rival and Quigg grazing Frampton's chin with a couple of flashing left hooks.
Frampton, demonstrating a better appreciation of distance, controlled the fourth as well, although Quigg did land with one thudding overhand right.
As the fifth rolled by, it was becoming difficult to work out what Quigg's game-plan was, other than to catch Frampton off guard with a big right hand.
There were a few boos after the sixth, which Frampton, boxing beautifully on the back foot, controlled again.
Quigg finally started taking a few risks in the seventh, but that only allowed Frampton to show off his defensive skills and pick him off on the counter.
Round eight was probably Quigg's, courtesy of a couple of big right hands and a sweet uppercut. However, he also missed with some wind-milling right hands.
The fight was finally cooking by the ninth, during which Quigg tagged Frampton with a juddering right hand and a strafing left hook.
The 10th was a tremendous round, with both men opening up, trading blows to head and body and doing extremely well not to buckle.
And the following round was more of the same, with some vicious body shots bookended by two more huge Quigg right hands, which clearly hurt his rival.
The previously bitter rivals hugged before the final round, which ended with Frampton showing off his Ali-shuffle, a sure sign he thought he had won by some distance.
In the chief support, Gavin McDonnell earned a unanimous decision over Panama's Jorge Sanchez to earn a shot at the WBC super-bantamweight title.
After his victory, the undefeated Doncaster boxer said he would like to fight the winner of Frampton-Quigg.
Also on the undercard, Manchester's Hosea Burton stopped Hertfordshire's Miles Shinkwin in round six to win the vacant British light-heavyweight title.
Morecambe's Isaac Lowe stopped Belfast's Marco McCullough to secure the vacant Commonwealth featherweight belt.
And former Commonwealth Games gold medallist Scott Fitzgerald won on his pro debut, the Preston light-middleweight stopping Swindon's Ben Heap in round three.
Carl Frampton beat Scott Quigg via a split decision in Manchester to add the WBA super-bantamweight title to the IBF title he already owned.