Earlier, having levelled at one set all, Murray misjudged a change in direction and fell in considerable pain making his quarter-final meeting with Andy Roddick an even tougher prospect.
But a medical time-out seemed to do the trick and in a high-quality final set, Murray made the decisive breakthrough when he chased down a smash to force Gulbis into a poor volley.
The Scottish star sealed a 5-7 6-1 6-4 win but remains a doubt for the rest of the Artois championship tournament.
His next opponent, defending champion Andy Roddick, went through when Mardy Fish had to retire with an ankle injury having lost the first set 7-6.
Talking to the BBC, Murray said: "My groin and neck are okay but the thumb is really sore. I'm pretty concerned about it right now.
"If I can't hold onto the racquet properly, and Roddick is hitting 140mph serves, that's probably not the best thing for a sprain, I guess."
In other matches, top seed Rafael Nadal won a surprisingly tough 6-4 3-6 6-3 against 18-year-old Kei Nishikori of Japan and David Nalbandian made short work of last year's Artois runner-up, beating France's Nicolas Mahut 6-4 6-1.
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