Iwamura tore the anterior cruciate ligament in his left knee last Sunday while trying to turn a double play against Florida and will surgery when the swelling subsides.
The Rays hope he will be ready to return in spring training. The AL champions hold a club option on Iwamura for next season.
"It was the most painful moment in my 13-year baseball career, and I knew something was wrong," the former star in Japan's Central League said through a translator before Friday night's game against the Minnesota Twins.
"It's getting better every day, little by little," he said. "My first intention is to get back to the field as soon as possible."
Iwamura was batting .310 with no homers and 16 RBIs in 44 games. He is in the final season of a $7.7 million, three-year contract he signed in December 2006.
Iwamura said although he has no control over whether the Rays exercise the option, he'd like to remain in Tampa Bay.
"I hope everything works out," he said, adding that it hurts "not only physically, but mentally" to not be in a position to contribute on the field for the rest of the season.
The 30-year-old was carted off the field in Miami after Florida's Chris Coghlan slid into him as the second baseman took a throw for a forceout and was ready to relay the ball to first with his left foot planted.
Iwamura, a five-time All-Star and six-time Gold Glove third baseman in Japan, said he watched a video replay and that there was no way for him to avoid the contact.
"I have nothing to say to Mr. Coghlan, but hopefully it doesn't happen again to other players," Iwamura said.
In addition to tearing his ACL, Iwamura damaged the medial collateral ligament in his knee and injured his left ankle. The MCL and ankle will not require surgery. He faces six months of rehab after the operation to repair the ACL.
"To get the surgery, I have to get the swelling down," Iwamura said, adding that a team doctor has told him the wait could be four to six weeks.