The Austrian head coach has agreed a three-year deal with the MLS franchise, who have met a buy-out clause inserted into his Reds’ contract.
Struber will leave after just ten-and-a-half months at the Oakwell helm, with Barnsley set to embark on the search for their fifth head coach in less than three years.
Assistant head coach Adam Murray is expected to take over from Struber in a caretaker capacity.
Speaking after Saturday’s game at Middlesbrough, Struber aimed a clear parting shot towards the club’s hierarchy after publicly questioning whether the owners ‘have the same ambitions and goals like me’.
The 43-year-old has grown increasingly frustrated at the club’s inability to sanction the signings he wanted, more especially up front following the sale of Jacob Brown and the inability to bring in a targetman.
In a radio interview with the BBC, Struber commented: “For me, it is not the goal to always play in the relegation zone.
“I have other ambitions and aims and I cannot feel that the owners have the same ambitions and goals like me. My future is open and we will see.
“Every year, every season, this is a big, big fight with a big, big energy until the last game to stay in the league. One more time, it is a big question to the owners, is this the goal? For me, no.”
Barnsley did bring in one forward ahead of last night’s international deadline in the shape of young Celtic striker Jack Aitchison, 20.
But he is viewed as a development signing and will join a League Two club on loan for the rest of the 2020-21 season.
The club announced two exits on international deadline day with Marcel Ritzmaier and Kilian Ludewig heading back to the continent.
Midfielder Ritzmaier has returned to Austria to join Rapid Vienna on a season-long loan.
The former Wolfsberger player, Struber’s first signing in January, has had a difficult spell at Oakwell. He is contracted at the club until June 2022.
Defender Ludewig, 20 – who only joined the Reds on a season-long loan in August – has returned to parent club Red Bull Salzburg and immediately joined struggling Bundesliga outfit FC Schalke in a separate loan deal.
Barnsley, with just one point from four Championship matches this term, return to action at home to leaders Bristol City on October 17.