Vilma, who was hurt in New York's loss at Cincinnati last Sunday, missed practice all week and was listed as out on the team's injury report Friday.
"This is a not a career-threatening injury and the doctors expect a full recovery," said Mitch Frankel, one of Vilma's representatives.
The loss of one of their defensive captains is the latest disappointing development in what has become a season full of them as the Jets have struggled to a 1-6 start.
"I am disappointed that my season ended prematurely," Vilma said in a statement. "I was looking forward to playing the rest of the season and helping the team get back on track. I now look forward to supporting my teammates for the rest of the 2007 season and returning to the field with them in 2008."
The Jets would not announce the exact nature of the injury or which knee is affected. The linebacker underwent several tests during the week and sought multiple medical opinions before deciding to end his season. He's still mulling his options regarding treatment.
"After reviewing all of the information available, the best thing for Jonathan and the Jets is to place him on injured reserve and turn his focus to rehabilitation and the 2008 season," general manager Mike Tannenbaum said.
"Vilma's a great player," Harris said earlier in the week. "Anytime that you lose a player like that, it's very hard to fill his shoes. He's a great team leader. He's very well respected and he has run the defense for four years now. I'll try to be ready when my number is called."
Since being chosen in the first round of the 2004 draft, Vilma has played in every Jets game and started all but two. He established himself as one of the best playmaking linebackers in the league and was selected for the Pro Bowl following his second season in 2005 after leading the league with 187 tackles.
The last two seasons have been a different story for Vilma, who has struggled along with a number of other players to be as effective in coach Eric Mangini's 3-4 defensive scheme. He was fifth on the team with 39 tackles.
"Jonathan is a leader and has always done everything he can to help this team win," Mangini said. "He's diligent in his preparation and has always unselfishly taken the time to share his knowledge of the game with his teammates. I know that he will approach this challenge with that same type of effort and focus."
Vilma spent part of the second half of last week's game on the bench and Mangini said Monday that Vilma, who had only three tackles, was "dramatically affected" by an unspecified injury.
During his weekly spot Tuesday on a sports radio station, Vilma said it was "a coach's decision" and wasn't due to any injury -- perhaps not wanting to violate the team's policy about not discussing injuries. On Wednesday, Mangini said he spoke to Vilma and explained the thought process, adding, "Sometimes you're going to see it differently as a player and as a coach. We'll just have to see how these tests go."
Copyright 2007 by The Associated Press.