Philadelphia general manager Paul Holmgren said Timonen was hit by a shot by Montreal's Andrei Markov late in Game 4 of Philadelphia's second-round victory over the Canadiens. Timonen had an MRI taken Wednesday that didn't show a clot, but a vascular surgeon found a small one Thursday.
"We have to view this that he's not a player for us in the series, and march on," Holmgren said Thursday night.
The Flyers eliminated the Canadiens in five games and will open the next series at Pittsburgh on Friday.
The nine-year veteran discovered the severity of the injury after a hospital visit Thursday morning. Timonen said the doctor told him if the clot improves in the next two weeks, there would be a small chance he could play again this season. Still, Timonen knows a return to the lineup is unlikely.
"It's the most disappointing thing in my hockey life, for sure," he said.
Timonen is the Flyers' top defenseman and played a crucial role in shutting down Washington's Alex Ovechkin for most of the seven-game, first-round series. Timonen was fantastic at anticipating plays, attacking Ovechkin with the puck and taking away space to create easy goals.
"How many times in your lifetime do you get to play in the conference finals or the Stanley Cup finals?" Timonen said.
Holmgren said Timonen, who didn't make the trip to Pittsburgh, is injured right where he ties up the skate.
"Obviously, you can't replace a player that does what Kimmo does for us," Holmgren said.
Timonen was also injured in Game 3 against the Capitals when he slammed into the net and crashed his right shoulder against the camera mounted inside. He didn't miss any games.
Timonen played Game 5 against the Canadiens, and felt numbness in his toes and foot that never went away. Timonen, who has six assists in the postseason, is on blood thinners. He had a similar injury earlier in his career with Nashville, but said that clot was much more painful and noticeable than this one.
Holmgren said the Flyers weren't taking any chances.
"If he gets hit again, a lot of problems could arise," he said.