Henderson (20-3) received winning scores of 48-47 and 49-46, and the other judge scored it 48-47 for Thomson (20-6). The announcement drew boos from the United Center crowd.
"Train this hard for this long, it's such a long camp and I see my title shot disappear," said Thomson, who fought most of the fight with a broken right hand. "This will probably be it."
Thomson and Henderson have been major players in the MMA lightweight division throughout their careers, but the fight was the first time they squared off.
Thomson controlled the first round, starting with a takedown and ending round with another fierce takedown, but injured his hand in the process.
The injury didn't appear to be a factor as the 35-year-old held his own against the former champ. Thomson also was spurned by a split decision in a fight against Gilbert Melendez in a Strikeforce fight May 9, 2012.
"The Gilbert fight that to me was a me a close fight, but I can say how it went either way, but this fight, I won with one hand. I beat the former UFC champion," Thomson said.
Thomson indicated to his corner after the second round that he thought he broke his hand.
Henderson came out aggressive in the third with a flurry of punches and a late takedown.
In the fifth, Thomson landed a right hand and a sweeping leg kick, then got a hold of a kick attempt by Henderson and pushed him into the side of the cage. Henderson was able to get in one last body shot at the end of the round that ended with some boos from the crowd.
"I think I definitely did enough to deserve to get my hand raised," Henderson said. "I like Ws. I like getting my hand raised, any way I can get it, by the skin of my teeth, by any means."
Henderson gave up the title after being submitted by Anthony Pettis on an armbar at UFC 164.
Henderson had a seven-fight winning streak going into the fight against Pettis, the second-longest run in lightweight history.
Henderson is aiming for a third fight against Pettis with the belt on the line this summer, but it is unclear if he will get that chance. On Thursday, UFC President Dana White wouldn't guarantee another rematch for Henderson against Pettis for the lightweight title if he won.
"I would say, my opinion in this matter counts for about that much, probably less than that," Henderson said. "It doesn't matter at all what I think or how I feel. It matters to D.W."
Henderson isn't worried how many fighters he will have to take on to get another chance at Pettis.
"I will take on the entire top 10. The entire top 10, bring them down."
Earlier, Stipe Miocic unanimously outpointed Gabriel Gonzaga in a three-round heavyweight fight. Miocic improved to 11-1, and Gonzaga dropped to 16-8.
Also, Donald Cerrone (22-6) rebounded from a loss to Pettis last year in Chicago by knocking out Adriano Martins in the first round. Cerrone struck Martins in the head with a right leg kick.