Elsom faces up to six-weeks on the sidelines after the seemingly innocuous training mishap on Thursday night.
The injury caps off a traumatic week at Waratahs headquarters following the news head coach Ewen McKenzie will not be returning next season.
"I didn't expect it (to be so serious)," Elsom said.
"Just yesterday at training it just popped when I took off and it didn't actually feel that bad.
"I had the scan last night and (discovered it is a) grade-two tear so it's a disappointment."
A dejected Elsom said the timing of the injury could not have been worse with a tough stretch of games on the horizon.
"(I am) very disappointed, it's such an important game for us (in the context of) this year," he said.
"I don't have to tell you how the ladder goes but if we lose it doesn't look that good."
But after an already eventful week, McKenzie took the bad news in his stride.
"We'll get through it," McKenzie said.
"It's just one of those things you deal with."
"You get injuries as you go along, it's unfortunate to have one late in the week but these things happen."
Blues coach David Nucifora labelled Elsom's loss as very significant.
"That's certainly a big blow for them," Nucifora said.
"He's a big contributor to their game and to their lineout so that's a loss for them."
Lock Dean Mumm moves to blindside flanker with Will Caldwell moving into the tight-five.