The bout, a rematch of the pair's 2011 "Fight of the Year," served as the headliner of Sunday's "UFC Fight Night: Shogun vs. Henderson 2," which took place at Ginasio Nelio Dias in Natal, Rio Grande do Norte, Brazil.
Rua looked crisp in the early going, using a barrage of leg kicks and sharp jabs to keep Henderson at bay and even wobbled him on a few occasions through the first two rounds.
But just when the 43-year-old Henderson looked to have nothing left in the tank, he shocked Rua with his patented power right hand, affectionately known to his fans as the "H Bomb." The shot landed flush, rearranging Rua's nose and sending him crashing to the canvas.
Henderson followed to the floor, and the follow-up blows forced referee Herb Dean to call off the fight 91 seconds into the third round. The much-needed result snapped a three-fight losing streak for the man most consider the best mixed-martial-artist ever to hail from the U.S.
"He definitely dinged me a little," Henderson admitted after the fight. "He rung my bell just a tad in the first round, also, and again in the second. I decided just to be patient. I wasn't very offensive, and that third round I think we both decided to get after it and leave things where we left them the first fight.
"I'm such a big fan of 'Shogun' and what he's done for the sport and how he represents himself in the sport. So thank you for bringing the best out of me, as well."
Along with the win, Henderson earned $100,000 in official UFC "Fight Night" bonuses for taking part in the "Fight of the Night" and being awarded one of the evening's "Performance of the Night" bonuses, as well. Rua also earned $50,000 for taking part in the "Fight of the Night."
In the night's co-feature, C.B. Dollaway (14-5) turned in one of the best performances of his career, downing former "The Ultimate Fighter: Brazil" winner Cezar Ferreira (3-1) in just 39 seconds.
Ferreira looked sharp on his feet early, landing with a power shot in the opening seconds. But Dollaway patently retreated to the fence and avoided follow-ups before unleashing a well-placed right hand that sent Ferreira tumbling to the canvas. Dollaway pounded with additional strikes, and referee Mario Yamasaki called off the fight in the opening minute.
"I love fighting down here in Brazil," Dollaway said. "The fans show incredible passion, and it is awesome to see I'm starting to develop a small fan base.
"I knew if I stuck to my game plan, I could control the fight and finish him, and that's exactly what I did."
A battle of lightweight winners of international versions of "The Ultimate Fighter" fell flat, as Norman Parke (19-2-1) and Leonardo Santos (12-3-1) fought to a majority draw.
While the bout was lacking in action throughout most of the 15-minute affair, it was an odd point deduction from referee Wernei Cardoso that ultimately led to the draw.
Cardoso penalized Parke one point for holding on to his opponent's shorts as he looked for a takedown in the second round. The call was made just as Parke appeared to be holding the cage in defence of that takedown, but Cardoso's decision was made.
The result was recorded as a majority draw, 29-27, 28-28 and 28-28, with Santos taking the opening round and Parke the final two on two of the three judges' cards.
Light heavyweights Fabio Maldonado (21-6) and Gian Villante (11-5) combined for a thrilling three-round contest with an incredible shift in momentum.
Villante took control of the action in the early going, utilizing his superior wrestling skills to secure the opening round.
He landed a knee flush to Maldonado's forehead in the second, opening up a cut that streamed for the remainder of the frame. But the wound only seemed to fuel Maldonado, who suddenly came alive with crisp combinations on the feet.
Villante returned to his grappling attack but was too tired to earn a takedown, leaving him to endure Maldonado's heavy hands for the remainder of the matchup.
Maldonado nearly finished the fight in the final minute, but Villante refused to quit, surviving until the bell. Maldonado was awarded the hard-fought unanimous decision with scores of 29-27, 29-28 and 29-28.
"It was a war standing up, but that was after he gave me a hard time on the ground," Maldonado said. "His wrestling is very good, so I knew I had to impose my striking game and avoid the fence. I knew that striking, he'd get tired first."
In a lightweight contest, Michel Prazeres (18-1) looked dominant in an impressive decision win over a heavily favored Mairbek Taisumov (21-5).
Prazeres was in control of the fight from start to finish, with powerful strikes and a strong wrestling game. The contest was marred by a pair of point deductions, as Taisumov repeatedly grabbed the cage in hopes of preventing a takedown.
But Prazeres didn't let the stoppage break his rhythm, as he cruised to a unanimous-decision win, 30-25 on all three judges' cards.
"I only have one thing to say: My team deserves a lot of praise," Prazeres said after the win. "The result speaks for itself. They did an amazing job."
The night's first main-card matchup ended in controversy when Brazilian featherweight Rony Jason (14-4) dropped Steven Siler (23-12) with a pair of powerful hooks.
While it appeared clear Siler was hurt, he also appeared to be defending as referee Wernei Cardoso stepped in to halt the fight just 77 seconds after it began. Unfortunately for a protesting Siler, the decision had already been made, and Jason was awarded a TKO win.
"I'm disappointed because it was an incredibly early stoppage by the ref," Siler said after the bout. "I didn't even have time to communicate I was OK because he jumped in so fast.
"I got hit, dropped to my back to take a defensive posture and was throwing an upkick to give me some space. And then, all of the sudden, it was over."