The 27-year-old's deal ties him to Warriors until May 2019, having joined in 2010.
Pyrgos, capped 18 times by his country, told Glasgow's website he had spoken with Dave Rennie, who will replace head coach Gregor Townsend next year.
"He told me about his vision for the club and his rugby philosophy and it's exciting," said Pyrgos.
"To have someone of Dave's quality coming in is brilliant for the club.
"I love everything about Glasgow Warriors and the club means a huge amount to me.
"This is my seventh year at the Warriors and winning the Pro12 two years ago has been the standout moment.
"I'm excited for the future here and we'll be working extremely hard to continue to compete for trophies every season. I believe we have a squad capable of doing that and that's the main reason I wanted to stay."
Townsend, who will become Scotland head coach next summer, added: "It's brilliant news for the club that Henry has signed for another two years.
"He is one of our leaders and has developed a huge amount in his time at the club. Now he is helping the club continue to improve and evolve on and off the pitch.
"There is a lot more to come from him on the playing side and we are really fortunate to have such a high quality group of scrum-halves right now."
Scotland scrum-half Henry Pyrgos has signed a new two-year contract with Glasgow Warriors.