The 28-year old Honduran midfielder lands in Texas in exchange for allocation money. Per league policy, terms of the deal will not be disclosed.
Rapids technical director Paul Bravo said: "The allocation money that we've gotten in this deal will give us flexibility to continue adding strength and depth to our squad.
"We had negotiated with Hendry during the offseason but ultimately we decided to move in other directions, so we're glad to get value in return at this point. He was an important part of our team over the last two years, and we want to thank him for his professionalism and contributions to our club."
Thomas, who has represented Honduras on 52 occasions, joined the Rapids from Wigan Athletic in August 2012 and went on to make 35 league appearances for the Denver outfit.
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