Jones, who at 23 became the youngest fighter in UFC history to win a title belt, stopped Rua at 2:37 of the third round on Saturday night in front of 12,619 fans at Prudential Center.
Despite the victory, Jones was placed on indefinite suspension pending an X-ray, MRI and orthopedic clearance of his right hand.
Rua is suspended 60 days due to the TKO. He is also suspended indefinitely pending a CT head scan.
Heavyweight Brendan Schaub is suspended 60 days for facial lacerations and indefinitely pending a CT scan of his facial/orbital bones. His opponent at UFC 128, Mirko "Cro Cop" Filipovic, is suspended 30 days after being knocked out and for facial laceration healing.
Filipovic is also suspended indefinitely pending a CT head scan. He was stopped by Schaub at 3:44 of the third round.
Light heavyweight Luiz Cane is suspended indefinitely pending an X-ray and orthopedic clearance of his left thumb. Cane's opponent, Elliot Marshall, was handed a 30-day suspension after suffering a technical knockout loss at 2:15 of Round 1.
Marshall is also suspended indefinitely pending a CT head scan.
Lightweight Edson Barboza is suspended indefinitely pending X-rays of his right hand and right knee. Barboza defeated Anthony Njokuani by unanimous decision.
Featherweight Raphael Assuncao was suspended 30 days after being knocked out at 2:32 of the first round by Erik Koch.
Franklin McNeil covers mixed martial arts and boxing for ESPN.com. Follow him on Twitter.