The Bears had just 9 yards in the first half and trailed 19-0 before David Montgomery had a pair of 1-yard TD runs to make it a one-possession game in the fourth quarter.
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But Philadelphia put it away with 16-play, 69-yard drive capped by Jake Elliott's 38-yard field goal. Wentz completed all four of his third-down passes on the drive for first downs.
The Eagles (5-4) have won two in a row after a pair of lopsided losses.
The Bears (3-5) have lost four straight.
Mitchell Trubisky was 10 of 21 for 125 yards and was sacked three times.
The Bears went three-and-out on their first five possessions, gaining minus-10 yards. They didn't get a first down until the final minute of the first half.
Wentz connected with Zach Ertz over the middle for a 25-yard touchdown pass to give the Eagles a 12-0 lead in the second quarter. Elliott missed the extra point wide right.
Howard ran up the middle 13 yards for a TD on the opening drive of the third quarter, extending the lead to 19-0.
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The Bears finally got going when Trubisky connected with Taylor Gabriel on a 53-yard pass to the Eagles 9 and Montgomery ran in from the 1. He leaped in from the 1 early in the fourth quarter.
But Chicago couldn't complete the comeback.
The Eagles had a first down at the Bears 5 on their opening drive, but settled for a 28-yard field goal by Elliott after Eddie Goldman sacked Wentz.
Elliott kicked another 28-yarder on the next drive to make it 6-0.
FAMILIAR FACES
Howard averaged 4.3 yards per carry in his first game against his former team. Jeffery had four receptions for 36 yards and at least two drops.
HEALTHY SCRATCH
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Eagles cornerback Sidney Jones, a second-round pick in 2017, didn't dress. Jones was projected to be a first-round pick before tearing his Achilles on his pro day. He has failed to live up to expectations in his two-plus seasons.
INJURIES
Bears: Goldman (thigh) left in the second quarter. ... LB Isaiah Irving (quad) was inactive.
Eagles: WR DeSean Jackson lasted just one series after returning to the lineup for the first time since suffering an abdomen injury in Week 2. He drew a pass interference on the first play and had a 5-yard catch. ... LT Jason Peters (knee) and LB Nigel Bradham each missed their third straight game.
UP NEXT
Bears: Host the Lions (3-3-1) next Sunday.
Eagles: Host the Patriots (8-0) on Nov. 17 after a bye.