The final results of diagnostic tests won't be known until Wednesday morning, but the expectation is that his foot injury is season-ending, a league source said Tuesday night.
ESPN NFL Insider Adam Schefter and ESPN.com's John Clayton were also able to confirm the news.
The Jets on Wednesday signed receiver Jason Hill, a source told Clayton. Hill had 25 receptions for 367 yards and three touchdowns for the Jaguars last season. Interestingly, Hill made headlines before the Jags played the Jets in 2011 when he said cornerback Darrelle Revis was "overhyped" due to the New York media. Hill ended up missing the game with a hip injury as the Jets beat the Jaguars handily.
The loss of Holmes would be a crushing blow for the Jets, who lost their best defensive player, Revis, nine days ago to a season-ending knee injury. Holmes is the team's leading receiver, generally regarded as their top playmaker on offense.
Holmes may have sustained a Lisfranc injury -- torn ligaments in the mid-foot area. That injury often requires surgery and takes several months of recovery time.
The Jets said Monday that X-rays were negative, but Holmes underwent an MRI exam -- and the results were forwarded to a foot specialist in Charlotte.
On Tuesday, the Jets announced they had nothing to announce. Rex Ryan is expected to reveal the diagnosis on Wednesday at his news conference.
Holmes was injured on the first play of the fourth quarter in Sunday's 34-0 loss to the 49ers. He caught a short pass in the flat and, as he turned upfield to run, his left foot got caught in the turf. He was transported out of the stadium on a golf cart, carrying crutches and wearing a walking boot on his foot.
Before signing Hill, the Jets had only three healthy receivers on the roster after they released Patrick Turner on Tuesday. Jeremy Kerley and Chaz Schilens are the starters, with Clyde Gates in reserve. Rookie Stephen Hill missed the last game with a pulled hamstring, as did tight end Dustin Keller.
Keller is likely to return for Monday night's game against the Texans.