The 23-year-old - stepping up two weight divisions - started in typically slow fashion but his power eventually told against the 'Magic Man', who produced a gutsy display in front of his own fans.
Malignaggi's slick movement and work rate was enough to take an early lead on the scorecards, although his punches - mainly to the body - lacked the venom necessary to trouble Broner.
'The Problem' did seem frustrated, though, and can count himself fortunate not to have had a point docked for thrusting a knee as well as a few elbows at his opponent in the second round.
However, once Broner landed his first meaningful blow in the third it seemed to blunt Malignaggi's footwork.
It was even heading into the seventh round and all the momentum was now with the challenger, although despite being accurate he was sparing with his shots.
Malignaggi refused to lie down, returning fire with some speedy combinations, but the more effective work continued to come from Broner.
When the bell rang in the 12th, the decision seemed inevitable, so it came as a surprise when it was announced that the three ringside judges could not come to a unanimous verdict.
After both fighters were scored 115-113 apiece, it was Broner who prevailed with a lop-sided 117-111 to become a three-weight world champion after just 27 fights.