During a tough performance in Sunday night's loss to the Gold Coast Titans at Skilled Park, Hayne received a severe cork on his shin.
The Blue and Gold fullback was also suffering soreness in the calf and back, and was ruled out of the match by the GIO City Origin doctor on Monday morning.
VIDEO: See Head Coach Ricky Stuart's heated response to the loss at Skilled Park
"I'm really disappointed, but I've pulled up pretty sore this morning," Hayne said.
"It was an honour to be selected in the City side and I wish the boys all the best, especially Tim.
"I'll certainly be supporting them."
Click through to see the full Country v City Origin sides as named on Sunday
Fellow Eel Tim Mannah was also named in the City side, and will join his City Origin teammates on Monday afternoon for a training session followed by a team visit to the Matthew Talbot Hostel.
Hayne's place in the City Origin side will be taken by young Wests Tigers fullback James Tedesco.
Sunday 21st April, 2013 - 3.04pm
Country Origin v City Origin
BCU International Stadium, Coffs Harbour
Updated: GIO City Origin Team:
Jamie Buhrer (18th man)
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