I didn't see it, but reader Jan from Wellesley tells me that happened:

Jeter was digging for third and Huckabay, the catcher had to come up the line and cover third. He got the ball as he came running in to the bag, and Jeter's left shoulder met his shin guard with full force, pushing the shoulder back. Jeter was in excruciating pain for some time as they tried to push it back in, and as they waited for a very long time for transportation out of SkyDome. It looks very bad -- Kaat and Murcer think he can be out for the whole season. They have this game on ESPN2 also, so I'm sure that ESPN will have more on it. Oh, and it was a clean, hustling play by Huckaby, and he looked quite upset when he saw the kind of pain Jeter was in. Sorry, I wasn't watching what Giambi did that led to Jeter racing toward third ...

Update: Jamie Wheeler adds some information:

I just thought I'd try to clear up what happened with Jeter's injury. He was on second and Giambi grounded out. Jeter broke for third, with the Jays being shifted for Giambi. Huckaby was paying attention and raced to third to cover. Jeter, Huckaby and Delgado's throw arrived at third at about the same time, and Huckaby slid to apply the tag, and his shin guard hit Jeter's shoulder.

They just updated it on Sportsnet, and it's a dislocated left shoulder, which was popped back into place at SkyDome. He is on his way to a local hospital.

Update: Daniel Shamah has one more fact to add.

Actually, he was on first when the play started. He took second on the
ground ball, and seeing that no one was covering third took a chance.
Huckaby was flying up the line to catch up and his left knee landed on
Jeter's left shoulder. He was writhing in pain for a good ten minutes.