The loss of Holmes is a major blow to the Jets already without top cornerback Darrelle Revis who is sidelined for the year with a knee injury.
Holmes was acquired by the Jets in a trade with Pittsburgh in April 2010 and he has played 32 games, catching 123 passes for 1,672 yards and 15 touchdowns.
The Jets have signed free agent wide receiver Jason Hill, previously with San Francisco and Jacksonville, to strengthen their receiving corps.
"Santonio is one of the top receivers in the game and it is a big loss," head coach Rex Ryan said.
"With that comes opportunities for other guys to step up. I believe as a football team, especially after that performance last week...we need to step up. I think you'll see improvement in our football team despite the loss of Santonio."
The Jets are 2-2 in the AFC East, alongside the New England Patriots and Buffalo Bills.