Wayne Rooney put United ahead but Craig Fagan leveled from the penalty spot for Hull, and it took Andy Dawson's own-goal to put the defending champions back in control. Dimitar Berbatov wrapped up United's win.
Chelsea, which hosts Fulham on Monday, is two points ahead of United but a resurgent Arsenal is just two points further behind.
"We are in a strong position," Arsenal manager Arsene Wenger said. "We can have belief, but it is a long way to go and we have to keep our feet on the ground and continue to improve together."
Wenger, though, could be without his captain for the next three weeks. Fabregas came on as a substitute but lasted just 27 minutes on his return following two weeks out with a hamstring problem.
Having replaced Denilson in the 57th, the Spain midfielder broke the deadlock in the 65th by curling a free kick beyond goalkeeper Brad Friedel's reach and swept in his ninth league goal of the season in the 81st.
Arsenal's Armand Traore seized on Milner's misplaced pass and picked out Theo Walcott on the right flank with a long diagonal pass. The England winger passed to Fabregas, who ran between two defenders before slotting home.
However, Fabregas then clutched his left hamstring as his teammates celebrated.
"It's a recurrence of his hamstring - we knew before the game it was not perfect," Wenger said. "I feel I did the right thing by gambling. I was cautious as well but I would do it again because sometimes you follow your instinct in a game."
Fabregas will undergo a scan tomorrow to discover whether he has pulled his hamstring again.
"If it's scar tissue, he will be out for just a few days. But if it's a pulled hamstring, it's three weeks," Wenger said.
At Hull, Rooney scored one and played a part in the three other goals.
The England striker put United in front in first-half stoppage time, turning in Darren Fletcher's cross.
Hull was gifted a route back into the game after Rooney's weak back pass allowed Fagan to nip in to win the ball. Fagan crossed to Jozy Altidore, and the US striker was bundled over by United defender Rafael da Silva. Fagan slotted in the penalty in the 60th.
"It was my mistake for the goal and I don't think the manager would have been too happy if we hadn't gone on to win," Rooney said. "It was a horrible feeling to let the lads down. I don't think it's happened to me before."
Rooney redeemed himself by whipping in the cross that Dawson inadvertently turned into his own goal in the 73rd.
Rooney helped to kill off the match nine minutes later by picking out Berbatov at the far post, and the Bulgaria striker tapped the ball into the net.
