Larry Holmes retained his heavyweight championship tonight when referee Harold Valan halted the bout with 44 seconds gone in 12th round and challenger Mike Weaver on his feet, but helpless to defend himself.

A crowd of 14,136 in Madison Square Garden was sensing a stunning upset before Holmes caught the challenger with a right uppercut near the end of the 11th round, knocking him down.

Weaver was up at the count of nine, about two seconds before the bell. Until then Weaver, a lightly regared underdog, appeared to be winning.

In earlier fights, Roberto Duran of Panama, the former lightweight champion, scored a unanimous 10-round decision over Californian Carlos Palomino, the former welterweight titleholder, and an overweight Jimmy Young (235 pounds) knocked out Wendell Bailey in the third round.

Holmes was listless, his reflexes were dull, and there was no snap in the punching that enabled him to go unbeaten through 30 previous bouts.

There were groans of disappointment from the fans when the referee stopped the action after Weaver had been down only once in the fight, but Dr. Edwin Campbell of the New York State Athletic Commission approved of Valan's decision, saying, "Weaver was not able to defend himself."

Holmes was measuring Weaver from the outset of the 12th and whipping in unopposed shots that snapped his head back or from side to side and the muscular Weaver was at a loss to do anything about it.

Young also defended the referee's decision. "If Holmes had not put him away in that round, it would have happened in the next (the 13th)," Young said.

Earnie Shavers, who will fight Holmes on Sept. 14 in East Rutherford, N.J., said to Holmes' pre-knockout performance, "I'll knock him out in five rounds."

Weaver had been decisioned by Rodney Bobick and knocked out by Duane Bobick and Holmes had predicted he would put away the former Marine from Los Angeles in four rounds.

Holmes slipped to the canvas in the fourth round shortly after being staggered by a right to the head. In the 10th, Weaver knocked Holmes across the ring into the ropes with a straight right to the head.

The challenger, 202, spotted Holmes 13 pounds and took command from the fourth through most of the 11th.

Referee Valan gave the fourth, fifth, and 10th rounds to Weaver; judge Tony Castellano the fourth, fifth, sixth and 10th, and judge Harold Lederman the third, fourth, fifth, 10th and 11th.

Duran knocked Palomino down in the sixth round with a quick right lead to the head and won the bout by 99-90 scores on all three officials' cards.

At 145 1/4, Duran was much stronger and even faster than Palomino, who weighed 145 3/4.

The Panamanian next is expected to challenge Jose (Pepino) Cuevas of Mexico for the World Boxing Association version of the welterweight championship.

Palomino is guaranteed a shot at the winner of the Sugar Ray Leonard-Wilfredo Benitez bout for the World Boxing Council welterweight champsionship on Dec. 1.

Duran took charge early and mocked Palomino's efforts with disdainful grins. Palomino was forced to hold as early as the fifth round and that was how he managed to endure. CAPTION: Picture 1, Larry Holmes slips to the canvas after being hit by challenger Mike Weaver. UPI; Picture 2, Roberto Duran, left, sends Carlos Palomino into the ropes during the first round of their fight. UPI