He won't depart the division as a champion, having surrendered his WBC and WBO world titles on the scale on Thursday when he failed to make weight for the bout in his home town of Newark.
But the American ended the week on a high, knocking the Brazilian down in the fourth round on the way to a convincing win, with two judges scoring the fight 117-109 for Stevenson and the third seeing it 118-108.
"I had a long week," said Stevenson, after improving to 19-0 with nine knockouts.
"I killed myself to make weight. All I wanted to do was come in and perform. I did everything I could to do that."
Conceicao, who won lightweight boxing gold at the 2016 Rio Olympics, could have captured the vacant titles after agreeing to go on with the fight.
Instead he falls to 17-2 with eight knockouts, his second defeat coming a year after he was on the end of a controversial loss to Oscar Valdez.
Stevenson dominated from the opening round before a crowd of 10,107, but he had a point deducted in the ninth when he slung Conceicao to the canvas.
"I think he was doing a lot of holding whenever I was getting on the inside," Stevenson said. "As soon as I got on the inside, he grabbed me.
"He was real awkward, he was real tough."
Stevenson came in 1.6 pounds over the 130-pound limit on Thursday, and said on social media he couldn't drop the extra weight without jeopardizing his health.
Now he's looking forward to moving up to the 135-pound division.
"I'm going to keep going up," he said.
