Referee Joseph Cooper deducted a point from Khan for pushing at the end of the seventh, and a second point in the 12th when Khan hit Peterson on the break.
Those deductions proved crucial when the scores were announced, one judge giving the fight 114-111 to Khan, but the other two scoring it 113-112 for Peterson.
“It’s like I was up against two people in there,” complained Khan. “(Peterson) kept trying to pick me up. He kept coming in with his head, lower and lower every time. He was being effective in pressing, but I was the cleaner fighter all night.
“I’m ready for a rematch. I knew it would be tough in his hometown.”
Khan (26-2) set the early pace with fast flurries and combinations, and scored a knockdown in the first round. Peterson (30-1-1) hauled himself back into the fight by stalking his opponent and digging hard body shots as Khan retreated to the ropes.
“It’s a 12-round fight, not a three-round fight,” Peterson said. “I wasn’t worried when I was knocked down.”
Khan got his second wind in the ninth, as the two men exchanged furious blows, but the final three rounds were close, with both men showing the effects of a grueling contest.
“A lot of people saw me as the underdog,” said Peterson.
“They didn’t give me a chance to win. I would definitely give him a rematch. He gave me a shot at the title, so I would definitely give him a rematch.”