The boxers nearly came to blows when tension between the fighters and their entourages sparked an hysterical outbreak of pushing and shoving that security officers had to break up.
Neither fighter was hurt, but Malignaggi's manager blamed the incident on the large Khan contingent in attendance and said the challenger would gain his revenge in the ring.
"There was some trash talking going on and they were in each other's face, and up to there I have no problem with it," Malignaggi manager Anthony Catanzaro, told Reuters.
"Then what happened was the Golden Boy (Promotions) matchmaker tried to get in between and push Khan away and divide the two fighters, and Khan pushed away."
Khan appeared to push away Malignaggi, who reacted angrily before the boxers were hauled away while the crowded room at the midtown New York hotel erupted in a chaotic scene.
Khan (22-1) tipped the scale at 139.5 pounds (63.3 kg), while former champion Malignaggi (27-3) came in at 139 pounds.
"We were told that the weigh-in was not open to the public, but obviously we were misinformed because there was a whole group of people there for Amir being loud and boisterous," said Catanzaro.
"Those are the people who bum-rushed the stage and pushed us all the way over to the other side," added Catanzaro, who credited Khan's father and uncle with acting as peacemakers.
(Additional reporting by Angela Moore and Brendan McDermid)
(Reporting by Larry Fine; Editing by Frank Pingue)