Jones, 26, ho has a central contract with the England Cricket Board (ECB), has committed himself to the County until the end of the 2007 season.
He was sidelined for six months after sustaining a ruptured cruciate ligament in his right knee during the opening Ashes Test in Brisbane in 2002 but battled back and was a member of the successful England's 2004/05 squad in South Africa.
Jones and Glamorgan clashed when he was left out of the side for some One-day matches last season prompting speculation the bowler, the son of former England left-arm quick Jeff, might quit his native County.
But Glamorgan chief executive Mike Fatkin said: "We're naturally delighted that Simon has committed himself to Glamorgan for the next three years.
"In addition to his high profile within the international game and his undoubted match-winning ability as a cricketer he is also perhaps the classic illustration of everything we're trying to do at the club in terms of developing home-grown players and doing everything we can to help them reach their full potential.
"His progress acts as a real role model for other younger players coming through.
"We're pleased that Simon sees his future with us and that he believes he can fulfil his potential with us. It's great news."
In 12 Tests, Jones has taken 36 wickets at a shade over 32 apiece.