It was a costly victory for San Francisco, which was already short-handed before losing Garoppolo to an ankle injury and Mostert to an injured knee. Defensive end Nick Bosa and defensive tackle Solomon Thomas were both carted off the field two plays apart with left knee injuries in the first quarter.
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The 49ers (1-1) also came in without star tight end George Kittle (knee), wide receiver Deebo Samuel (foot), cornerback Richard Sherman (calf) and defensive end Dee Ford (neck).
It didn't matter against the Jets (0-2), who have also been hit hard by injuries and couldn't muster much. Now, the defending NFC champions head into Week 3 with some serious concern for key players.
The 49ers got going early against the Jets, Mostert taking a handoff on the first play, zipping outside and taking off down the right sideline untouched for an 80-yard score.
The strange silence of the eerily empty MetLife Stadium _ without anyone in the stands because of the coronavirus pandemic _ surely mirrored what it would have sounded like if stunned Jets fans were in attendance.
Garoppolo was injured on the 49ers' next drive when he was sacked by Quinnen Williams. The quarterback went down awkwardly and needed his right ankle taped, but he remained in the game until halftime.
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Things got a lot worse for the 49ers a few minutes later.
Bosa was carted off the field with a left knee injury. Last season's NFL Defensive Rookie of the Year appeared to have his left leg bent behind him at the end of a 4-yard run by Frank Gore with 6:22 left in the first quarter.
Two plays later, Thomas needed to be carted off also with a left knee injury after an 8-yard reception by Chris Hogan. Like Bosa, Thomas was ruled out for the rest of the game.
Sam Ficken's 41-yard field goal cut the deficit to 7-3 for the Jets, but Garoppolo limping noticeably drove the 49ers for another TD.
Mostert nearly had another long touchdown on the second play of the drive, but his 67-yard scamper was wiped out by a holding penalty on tackle Mike McGlinchey. But San Francisco ended the 14-play possession with an 18-yard catch by Jordan Reed, who leaped over a diving Marcus Maye to get into the end zone.
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The Jets had a promising drive ended when they went on fourth-and-1 from the 49ers 20 and Josh Adams was stuffed for no gain. New York wide receiver Breshad Perriman injured his left ankle early in the drive and didn't return.
The 49ers took advantage as Garoppolo marched them 80 yards for another score, a 4-yard pass to Reed, his second of the game, with 11 seconds left in the half. The drive was prolonged by a roughing-the-passer penalty on Henry Anderson when the Jets appeared to have stopped San Francisco on third-and-8.
Garoppolo was 14 of 16 for 131 yards and the two TDs before being replaced by Nick Mullens.
The 49ers started slowly on Mullens' first drive, but Jerick McKinnon had a 55-yard run on third-and-31. The last team to convert a third down that long on a run was Minnesota on Leroy Hoard's 53-yard scamper on third-and-37 against Denver in 1999.
Robbie Gould's 46-yard field goal made it 24-3 midway through the third quarter. McKinnon's 16-yard TD run gave San Francisco a 31-6 lead.