O'Neal had 24 points and 10 rebounds in his return to the lineup for Miami. He started for the first time since Dec. 26, when he aggravated a previous hip injury, missing eight games in that stretch. O'Neal fouled out for the sixth time this season.
"It's the same old thing, we just need to get it together," O'Neal said. "Offense is not a problem. We need to stop somebody."
After making only two of his first nine shots, Dwyane Wade finished with 24 points.
Luol Deng had 21 points and Andres Nocioni rebounded from an injury in Tuesday's loss at Orlando to score 20 points. Thabo Sefolosha scored a season-high 17 points for the Bulls, whose 126 points were a season high.
Jason Williams scored 17 points and Udonis Haslem had 15 for Miami, which has hit a new low in a down season, seemingly with no end in sight.
"That was as complete a loss as you can have," Heat coach Pat Riley said. "The team didn't quit, it's just bad. ... When you give up 126 points defensively at home and you've already lost 10 in a row, it's bad. I have now, tonight, at this moment, no answers for it."
The Heat's last win was Dec. 22, 104-102 over Utah.
"We lose every time," Wade said. "We lose and it's a fact of life. It's not easy."
Miami pulled to 62-60 at 9:03 of the third, but the Bulls went on a 10-3 run and never looked back, taking a 93-79 lead into the fourth period.
"It was a much needed win after two tough losses," Sefolosha said. "We came out ready to play and did the job throughout the game."
Nocioni hurt his hip in the third quarter of Tuesday's game after he fell on his back and had to be helped from the court. He didn't show any after effects of that injury.
"I feel much better after I loosened up a little bit," Nocioni said. "It's going to hurt tomorrow but there's nothing broke and I'm going to be ready for the next game."
The Bulls were missing another starter. Guard Kirk Hinrich missed his second straight game because of back spasms.
With O'Neal's presence in the lane, the Bulls went to their perimeter shooting game in the first period. Seven of their first eight field goals came from outside.
"I'm really pleased with the way our guys responded," Bulls coach Jim Boylan said. "It has been a tough week for us and a tough road trip. With all that's been swirling around us we didn't want to go home with another loss. This is nice for the guys."
Miami outscored Chicago 30-24 in the second period, cutting the Bulls' lead to 58-53 at the half. O'Neal had 18 points in the first half, his best half of the season. Smith had 17 first-half points for Chicago.
"We played with a lot of pride," Smith said. "We felt the last two games [losses at Atlanta and Orlando] were very disappointing for us and our fans to watch in Chicago. We just wanted to play and be aggressive on both ends of the floor. We wanted to get some momentum going home."
The Bulls closed out the first quarter with a 14-5 run to take a 34-23 lead.
It was the first meeting between the teams since Chicago swept Miami in the first round of last year's playoffs. ... Joakim Noah and Ben Wallace were reported to have had an argument during Tuesday's game at Orlando, but Bulls coach Jim Boylan downplayed the incident before the game Wednesday night. Neither player commented, and they stood next to each other during the pre-game National Anthem. ... Miami is 2-23 when trailing after three quarters. ... Miami's Alonzo Mourning, out for the season because of a knee injury, sat on the Heat bench.