It will leave the Cowboys talisman stranded on 299 NRL games - he was due to chalk up his 300th on a night of celebration against the Panthers on Saturday night - until 2018.

In a huge blow for Queensland and the Cowboys' title aspirations, Thurston will require surgery on a shoulder injury that restricted his performance in game two - joining Darius Boyd (broken thumb) as notable omissions from the Maroons line up for game three.

"Given it was already an injured shoulder, the club and the player decided he had to undergo surgery immediately, effectively ending his season for 2013," Cowboys coach Paul Green said.

Thurston said he had originally hoped the injury was just a cork, before scans on Thursday revealed the worst.

"The news isn't good," Thurston said.

"And the best decision for myself and the club is to get the op done. I thought I might have been able to pump one or two more games out.

"But the medical advice I've been given is that if I wanted to live a normal life after football, then I had to have the surgery."

He was visible in pain for much of the Maroons' come-from-behind 18-16 win on Wednesday night and was due to be farewelled from Queensland colours in front of a heaving Suncorp Stadium in the decider. He will also miss the World Cup.

Thurston, who earlier in the year announced this would be his final Origin series, will finish his time with the Maroons on the back of a match-winning sideline conversion that kept the series alive at ANZ Stadium.

But the Maroons and Kangaroos veteran added he would have no second thoughts on his decision to retire from representative football.

"It's a decision that I've made," he said.

"I wanted to finish on a high this year with representative football. I'm comfortable with that decision I've made to retire from rep football."

Fairfax Media understands his Cowboys teammate, Michael Morgan, is likely to get the nod at five-eighth for the decider ahead of Daly Cherry-Evans and Corey Norman.

In Thurston's absence in game one, it was Anthony Milford who donned the No.6 jersey however the Broncos playmaker is also sidelined through injury.

Morgan's likely promotion from the interchange to the starting side will open up a utility spot on the bench. Melbourne's Cameron Munster is likely to come into calculations given his relationship with the Storm players as well as the fact he can play almost everywhere in the backline.

But the biggest blow will be for the Cowboys, for whom Thurston has played just seven times this season after sustaining injures in the Anzac Test and Origin II.

Cowboys coach Paul Green is expected to confirm the news on Friday.

Bookmakers immediately slashed NSW's chances of winning the series on the back of the Thurston update while North Queensland has drifted in premiership betting.

with AAP