The team announced that the 2012 first-round pick has signed a two-year deal, worth a total of $6 million.
General manager Kevin Cheveldayoff isn't sure when Trouba will rejoin the team or be in the lineup.
His agent claimed the situation was not about money, but Trouba's desire to play as a top four defenceman with the Jets on the right side.
Trouba will count $3 million against the salary cap for the remainder of this season and next.
Trouba, who originally requested a trade, will earn $2.5 million U.S. this season and $3.5 million in 2017-18.
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The Rochester, Mich., native has played 211 regular-season games with Winnipeg and has 23 goals and 72 points.
The No. 9 overall draft pick in 2012, Trouba made a quick jump to the National Hockey League and has already amassed 72 career points in 211 games. Still, he was selected to the World Cup's Team North America and is widely considered one of the best young defencemen in the game. Trouba's agent Kurt Overhardt, represented Ottawa Senators forward Kyle Turris when Turris held out from the Arizona Coyotes five years ago and requested a trade.
The Jets had significant leverage because they owned his rights, but Trouba's absence and an injury to defenseman Tyler Myers tested the team's depth.
"We've been interested in signing Jacob all summer and certainly I think the statement we made during this process was we're going to continue to look at an opportunity to bring Jacob back into our fold and be a part of our future and a big part of our future", Cheveldayoff said.