Jeter will go on the disabled list and be sidelined for at least two weeks, New York manager Joe Torre said after the Yankees' 8-4 win. But the extent of the injury wasn't immediately clear.
"This isn't getting hit by a pitch or spraining an ankle," Jeter said. "Hopefully, there's nothing wrong."
Jeter was injured in the third inning on a headfirst slide into third base.
"There's nothing broken, but they still have to take an MRI," Jeter said.
Jeter was down for more than 10 minutes Monday, writhing in pain and surrounded by worried teammates. He was helped onto a cart by trainers Gene Monahan and Steve Donohue, strapped in place sitting upright and taken off the field - his head bent, his face dripping with sweat.
"It hurts. I can't really describe it," Jeter said. "The worst part is getting it back in."
The shoulder was popped back in place and Jeter was taken to a hospital for X-rays.
"I think no question it will be a DL. How long it takes beyond the initial two weeks, we don't know," Torre said. "I think the X-rays were OK. The good thing that happened is it was the left shoulder."
The five-time All-Star has been the Yankees' leader during their run of four World Series titles and five AL pennants since 1996.
"He's a big part of what we do, emotionally," Torre said. "The numbers he puts up are sort of icing on the cake. It's what he gives us, a presence."
Jeter was trying to advance an extra base on Jason Giambi's comebacker, an attempt to take advantage of Toronto's defense, which was shifted to the right side of the infield.
Huckaby ran up the line to field first baseman Carlos Delgado's throw. Jeter dived headfirst into the bag, and Huckaby fell, his shin guard driving into Jeter's shoulder.
Jeter immediately began writhing as Yankees' trainers, teammates and manager Joe Torre gathered around.
Dr. Erin Boynton and Dr. Ron Taylor of the Blue Jays also came out to help Jeter, while Huckaby watched anxiously from the dugout with a towel in his mouth.
Jeter was called out on the play because he fell off the base when he was hurt.
On Sunday, Yankees manager Joe Torre talked about how much healthier Jeter looked this spring and that he seemed "free and easy" at the plate.
It was a difficult spring for Jeter. Owner George Steinbrenner publicly questioned his "focus" in the offseason and said he was worried that off-field activities detracted from on-field performance.
Jeter hit a career-low .297 last season with 18 homers and 75 RBIs. His batting average has dropped three straight years, from .349 in 1999 to his first sub-.300 average last season.
Jeter has said part of his problems could have been caused by a right shoulder injury that prevented him from doing upper-body work in 2001 and 2002.
Jeter has been very durable in his career, playing through a variety of nagging ailments and has even tried to hide injuries from Torre so he could stay in the lineup.
He has been on the disabled list only three times in his career, never for more than 16 days at a time.
By Josh Dubow