Both players would have been free to leave in the summer with Crouch linked with a possible move to QPR and Whelan linked with a reunion with Tony Pulis at West Brom.
However the Potters have been holding discussions with the players for some time and the experienced pair have now ended speculation about their future, much to the delight of Stoke boss Mark Hughes.
“It’s pleasing that both want to stay and be a part of what we are striving to achieve at the club,” Hughes told the club’s website.
“They are both fantastic professionals who had contributed a great deal to Stoke City long before I joined the club and have continued to do so. I’m delighted they are staying with us for at least another couple of years.”
Chief executive Tony Scholes said: “Players like Glenn and Peter are very much the backbone of our squad.
“They have both proved to be fantastic signings for Stoke City. The experience they bring to bear on the side, both on and off the pitch, cannot be underestimated and they still have so much to offer.”
Whelan and Crouch have amassed more than 350 games between them during a combined service of more than 10 years at the Britannia Stadium.