Trescothick, who has agreed to take over as Somerset captain from Justin Langer in 2010, was first affected by the illness on England's tour of India in 2005-06.
The 33-year-old was then forced out of the Ashes tour the following winter only two weeks after leaving home and the problem eventually forced him into international retirement.
Somerset had hoped that the special measures they had put in place for Trescothick, including travelling out to India with his wife, would enable him to spearhead their drive for success in the lucrative Twenty20 Champions League.
"Marcus deserves a huge amount of credit, it was a courageous decision for him even to try to go there to play," said Vaughan.
"It's obviously not worked out but I spoke to him this morning (Friday) and he's fine. It's not the first time this has happened but at least he's given it a go.
"I didn't speak to him about the details, I just called to make sure he was all right. It was obviously bad enough for him to come home and he knows what his own limits are."
Somerset chairman Andy Nash told BBC Sport that Trescothick was "fine" when he spoke to him on Friday.
Somerset boss reassured about Trescothick
"He sounds like normal Marcus, down to earth and grounded," said Nash.
"Everyone connected with the club and cricket is aware how brave it was of him and (his wife) Hayley to even travel out there in the first place.
"This is not a step back for Marcus. It was a victory for him to get there.
"We are full of admiration for what he has done for us. We are looking forward to him being a highly successful captain for us from next season."
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