Javid Bowen will now slot onto the wing for Winterstein.
But the jury is out on whether Linnett will return from a hamstring complaint that sidelined him for the sudden death semi-final.
North Queensland coach Paul Green described Linnett as "likely" to play the grand final qualifier in a reshuffled backline.
Cowboys under 20s star Ponga still flew out with the team on Wednesday.
"Kalyn is coming down as cover for Kane," Payten said.
"The coaches believe it's also a good experience for Kalyn to see how we do things travelling away and being in the finals system.
"But we expect him to run out for the 20s."
Cowboys coach Paul Green said Linnett will be given every chance to take the field against the Sharks.
"He's worked hard doing everything he can around the clock to get back in," Green said.
"He (Ponga) didn't let anyone down last week, he did a good job on his debut.
"(But) he is there as back-up."
The Cowboys under 20s play reigning premiers Penrith in their own Friday night preliminary final.
Ponga - just 18 - became the sixth player in 30 years to make his NRL debut in a final after being a shock call up for Winterstein against Brisbane.
But Ponga belied his age to amass 174m, two tackle busts and a line break, almost scoring with his second touch.
He has already earned the "next Johnathan Thurston" tag.
Ponga got the thumbs up from the man himself.
"He's obviously got a big future at the club," Cowboys co-captain Thurston said of Ponga.
"He's come through the system.
"There's a genuine pathway and players can now aspire to follow him."
His impressive debut has ensured the Cowboys will begin off-season contract extension talks, despite Ponga's current deal not expiring until the end of 2017.
Rival NRL clubs as well as rugby union and even the AFL's Brisbane Lions are believed to be ready to pounce.
- AAP
