Bosa went down with the injury after a first down run from Jets running back Frank Gore. Bosa was visibly in pain on the turf before trainers carted him to the locker room.
Two plays later, the 49ers lost Thomas after getting tangled up with Jets offensive lineman George Fant.
Both players were quickly ruled out of the game shortly after leaving the field.
Bosa, 22, was selected by the 49ers as the second overall pick in the 2019 NFL Draft and became one of the league's top defensive players during his rookie season. Bosa totaled 42 tackles and nine sacks as a rookie and won the NFL's Defensive Rookie of the Year award as well as a spot in the 2019 Pro Bowl.
Thomas, 25, is in his fourth season with the 49ers after being selected with the third overall pick in the 2017 NFL Draft. After totaling 81 tackles and six sacks over his first three seasons, Thomas headed into the fourth and final year of his rookie contract hoping 2020 would finally be the breakout season he and the 49ers have been waiting for since 2017.
The 49ers were already down two defensive linemen with Dee Ford out due to a neck injury and Ronald Blair on the physically unable to perform list as he continues his recovery from a torn ACL that ended his 2019 season. The team has shown interest in free agent defensive end Ezekiel Ansah but the two sides have not come to terms on a contract.
The 49ers were also playing Sunday without cornerback Richard Sherman (calf), wide receiver Deebo Samuel (foot), and tight end George Kittle (knee).
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