Thomson requires surgery to rectify the problem and will therefore be out of action until October.
"I'm gutted at missing out on the chance to compete at the World Cup," said Thomson.
"My focus will be on working hard with the Glasgow physios on my rehab so that I can be back challenging for a place with the Warriors as soon as possible."
Thomson has been close to an ever-present in the Glasgow matchday squad this season, missing just three of his side's 22 Magners League matches.
He is now just six games shy of a century of Magners League appearances but will miss the start of the new domestic season.
Thomson appeared in the 2007 World Cup in France but is currently behind Edinburgh's Ross Ford and Gloucester's Scott Lawson in the international pecking order.
But with the possibility of selecting three hookers for the global gathering in New Zealand, Scotland coach Andy Robinson has described Thomson's injury setback as 'disappointing news'.
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