Though Broner failed to back up his pre-fight boast that he would knock Malignaggi out in front of his home crowd, he overcame a slow start to land some ferocious blows in an entertaining bout throughout which he taunted his opponent, saying repeatedly: "You can't hit me."
Broner did enough to win over two of the three judges, with the scorecards reading 117-111 and 115-113 for Broner and 115-113 for Malignaggi.
The 23-year-old, whom most ringside analysts called as a clear winner, improved his unbeaten record to 27-0 while Malignaggi fell to 32-5.
Broner landed 246 of 524 punches while Malignaggi landed 214 of 843. Though Malignaggi was busier, his opponent landed more shots and inflicted greater punishment.
However the decision enraged the 32-year-old Malignaggi who alleged Broner's manager had one of the judges "in his pocket" and threatened to retire if he did not get a rematch.
"I thought I out-threw him and outworked him," Malignaggi said.
"He was sharp in spots, but he wasn't busy. He didn't land. They looked pretty. When he did work, he was good, but I had the better pace. This is a close fight. I don't even mind having him close or me close. But it could have gone either way.
"In my hometown, as the defending champion, I felt like I should have got it. Tom Schreck is a New York judge and in Al Haymon's pocket. That's all there is to it."
He added: "I'm not saying it was fixed, but it's always the more connected fighter who gets the decision."
Broner said: "He's a world-class fighter and I respect him. To come to somebody's hometown and beat them on a split decision, that's saying something. This was a tremendous win for me. I mean, who's doing it like me? Nobody.
"I came into town and I got his belt and his girl."