Jefferson got hurt while corralling his final rebound. He went down clutching his back with 1:29 left and had to be helped off the court in obvious pain. Team officials said he had back spasms.
Jefferson had just eight points at halftime but scored 17 in the third quarter and was the difference down the stretch as the Jazz held off a furious Orlando comeback attempt.
Orlando trailed by 14 in the first half and by 11 entering the fourth but took a 79-78 lead on Glen Davis' powerful jam. Randy Foye's 3-pointer and back-to-back jumpers by Jefferson sealed the win for Utah.
Davis led Orlando with 18 points. Jameer Nelson had 17 and Arron Afflalo added 16.
The Magic managed just 15 points in the first quarter and 34 in the first half, but fought back behind Davis.
His three-point play pulled Orlando to 76-72 with 5:41 remaining and J.J. Redick's three-point play off a driving layup with 4:20 left had the Magic within 78-77. Davis' powerful dunk over two defenders gave Orlando a 79-78 lead with 3:33 left.
Foye, who started 0 for 5, countered with a 3-pointer to put the Jazz back on top 81-79 with 3:11 remaining, and Jefferson's 5-footer bumped it to 83-79.
Jefferson finished 13 of 20 from the field with two assists and a steal.
He started with a hot hand in the third quarter, but the Jazz quickly cooled off after taking a 56-45 lead following Jefferson's 5-footer in the lane. Orlando scored the next eight points, including a pair of baskets by Redick, as the Magic pulled to 56-53.
Utah closed the quarter on a 12-4 run to lead 68-57, with Jazz reserves providing the spark defensively. DeMarre Carroll had a pair of steals and helped force a backcourt violation. Jefferson was Utah's offense with a 17-point quarter on 6-of-9 shooting.
Overall the Magic shot slightly better but Utah's only 3-pointer of the night, by Foye, made the difference.
The Jazz held Orlando to 15 points in the first quarter and 34 in the first half, limiting the Magic to 36 percent shooting and forcing a dozen turnovers.
Utah also held a huge advantage on points in the paint (30-14) in the first half, with Jefferson and Paul Millsap doing much of the damage.
Jefferson had six points, seven rebounds and an assist in the first quarter. Millsap, meanwhile, had surpassed his season average (13.9 points) by halftime, with 11 of his 16 first-half points coming in the second quarter when he shot 4 of 6. He also had three blocks, a pair of assists and a steal in the half.
Despite the mistakes, the Magic pulled within five in the second quarter on a layup by Andrew Nicholson. But the Jazz went on an 11-4 run, with backup point guard Earl Watson and Millsap pushing the pace. Millsap scored seven straight points for Utah and Marvin Williams capped the run with a layup off a nice pass from Jefferson.
The Jazz led by as many as 14 late in the second quarter and held a 45-34 lead at the break - the 34 points being an opponent first-half season low for Utah.
Utah got an early boost from Williams, back in the starting lineup after missing the previous three games with concussion-like symptoms. He had been averaging 10.4 points a game and finished with eight.