The tight-head prop, who made his Scotland debut against Italy in last year's Six Nations championship, has made 70 appearances for the Warriors since joining them from amateur club, GHA in 2008.
The 26-year-old was called up to the Scotland squad for this year's Six Nations championship and last month played for Scotland A in their win over England.
Jon Welsh said: "I am very happy to have committed my future to the Warriors and I am looking forward to playing my part in bringing success to this club.
"It has been a frustrating season for me having missed several months through injury, but now that I'm back to full match fitness I am looking forward to being involved in the remaining games this season.
"We have a really strong squad, who all work hard for each other and the facilities at Scotstoun are excellent, so this was a really easy decision for me to make."
Glasgow Warriors head coach Gregor Townsend said: "This is excellent news for the club and it will give our squad a big boost ahead of some hugely important games.
"Jon worked hard during his injury lay-off to build up his strength and has been putting in the hours in recent weeks to get back to full fitness. He is respected by both coaches and players and is a key part of our future.
"Jon has shown that players from the club game can make the jump to professional rugby and he should be an example to others looking to make the breakthrough.
"We're delighted to keep him at Scotstoun for the next couple of years and he will undoubtedly have a big role to play."
Meanwhile, 90% of the tickets available for this Friday's game at Scotstoun Stadium between Glasgow Warriors and Munster (kick-off 8.05pm) have been sold. Tickets are still available to buy online and print at home from www.glasgowwarriors.org.
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