Whelan out for four to six weeks
Whelan sustained the injury while on international duty with the Republic of Ireland and had to be withdrawn early in the second half of the 1-1 draw with Germany.
The 30-year-old had previously started every Premier League game this season, but was forced to miss Sunday's 2-1 win over Swansea City, and manager Mark Hughes confirmed on Thursday that Whelan had sustained a fracture.
"Glenn unfortunately has a fracture in his leg," the Welshman said. "He picked it up in the international game.
"There is a slight fracture, but he hasn't been put into a plaster cast. We feel that he can come back sooner by avoiding that.
"It is a blow for him and it is a blow for us because we are likely to be without him for four to six weeks. It is disappointing but thankfully we have options in there."
Swansea manager Garry Monk felt aggrieved at the award of Stoke's equalising penalty in the clash at the Britannia Stadium, and accused Victor Moses of cheating for his part in the incident.
Hughes was less than impressed with Monk's remarks, and the Football Association announced on Thursday that they had contacted the Swansea boss regarding the situation.
"I think it's right the FA ask Garry to clarify his comments," Hughes said. "I made my feelings known, it's a fairly strong view. It's disappointed me because it's overshadowed a good performance.
"Second half we deserved to win the game anyway. We would have won the game anyway irrespective of the incidents that have had so much attention.
"Garry is a very articulate young man but maybe on that occasion used the wrong words. That can happen. Victor says he felt body contact and was impeded. Photos have verified that."