Henderson defended a double-leg takedown in the third round by applying an arm-in guillotine choke to force a quick tap out at two minutes and 41 seconds.
"As soon as I couldn't get my hands under there [to defend]," Varner said. "I knew I was done."
It was a tough loss for Varner, who returning after a year-long absence, was winning the fight until he was caught in the choke. Varner, a former UFC lightweight, was the stronger fighter and the aggressor against the interim champ.
"I came to fight, Ben was the better man," Varner said. "Caught me in the guillotine. He had a strong guillotine. I wanted to box, he wanted to kick. S--t happens."
In the co-main event, hometown favorite Urijah Faber earned himself a title shot against Jose Aldo by submitting Raphael Assuncao with a rear-naked choke at three minutes and 49 seconds of the third round.
"It was a small mistake scrambling," Assuncao said. "I thought I would be able to get out of it, by giving up my back and controlling his wrist."
At the post-fight conference, WEC general manager Reed Harris confirmed Faber as Aldo's next opponent.
"I'm ready to get that belt," Faber said. "We got a great champion right now. Jose Aldo. He's a phenom. He's both talented and creative. I'd love to go in there and get that belt."
Faber received the Submission of the Night award, a $10,000 bonus to his purse.
Former Olympic wrestler Kamal Shalorus dominated Team Quest fighter Dave Jansen in the wrestling department and rocked the Team Quest fighter several times for the unanimous decision victory. With scores of 30-27, 30-27 and 29-28, Shalorus handed Jansen the first loss of his career.
Former champion Mike Brown quickly dispatched of WEC newcomer Anthony Morrison with a rear-naked choke at one minute and 54 seconds of round one. Brown said he wants to face the winner of Faber vs. Aldo, but will look to accept the risk to fight rather than sit and wait for a title shot.
Former IFL title challenger Deividas Taurosevicius knocked off top ten ranked Mackens Semerzier with three 29-28 scores, sealing the unanimous decision by controlling the first two rounds of the fight.
Notes: Will Campuzano and Coty Wheeler were each given a $10,000 for participating in the Fight of the Night ... No fighter won the Knockout of the Night award since no one fight ended in a (T)KO ... The WEC is still planning on a pay-per-view sometime in the first half of 2010 ... "Nothing concrete" yet on a The Ultimate Fighter-type reality television show on Versus.
Ben Henderson def. Jamie Varner by third-round submission (live blog)
Urijah Faber def. Raphael Assuncao by third-round submission (live blog)
Kamal Shalorus def. Dave Jansen by unanimous decision (live blog)
Mike Brown def. Anthony Morrison by submission (live blog)
Deividas Taurosevicius def. Mackens Semerzier by unanimous decision (live blog)
Charlie Valencia def. Akitoshi Tamura by split decision
Wagnney Fabiano def. Clint Godfrey by unanimous decision
Mark Hominick def. Bryan Caraway by first-round submission
Eddie Wineland def. George Roop by unanimous decision
Will Campuzano def. Coty Wheeler by unanimous decision