Manly overcame a major scare to easily eliminate North Queensland from the NRL finals series on Saturday night with an emphatic 42-8 victory at the Sydney Football Stadium.

The Cowboys surged to an 8-0 halftime lead which had the Warriors and St George Illawarra sweating bullets about their safety in the McIntyre System.

But in the end the Sea Eagles big guns, namely doubles to Brett Stewart and William Hopoate, got Manly home with a 42-0 second-half shut-out.

In the lead up to the match, the Sea Eagles made no secret of the fact they were filthy their home final would be held away from Fortress Brookvale, where they haven't lost a match all season.

Their disappointment was in a way justified, with just 13,972 fans turning out - far less than the 23,000-capacity of Brookvale Oval.

The Cowboys seized upon the less abrasive atmosphere of the neutral venue and in the first half their defence was as strong and resilient as it's been all season.

North Queensland ace Johnathan Thurston made his best start to a match since returning from a serious knee injury in round 23, kicking a penalty and laying on the opening try to Willie Tonga with a well-placed grubber.

But it was from a rare Thurston mistake that Manly finally got on the board in the 48th minute and they never looked back.

The Cowboys No.7 tried to give Matt Bowen an inside ball on the Manly 40 metre line, but the ball went astray and Sea Eagles second-rower Shane Rodney streaked away upfield.

Although he ignored an unmarked Jamie Lyon on his inside, Manly made the most of the field position, when a scrum move resulted in winger Hopoate powering over in the right corner.

The Sea Eagles stormed to the front for the first time on the back of a stunning try to fullback Stewart from a Kieran Foran around-the-corner ball just nine minutes later.

Dally M rookie of the year Daly Cherry-Evans was involved in nearly everything as Anthony Watmough, Jamie Buhrer, Hopoate and Matt Ballin crossed in a late flurry which earned Manly a week off.

The Dragons are now safe and, if Melbourne beat Newcastle as expected on Sunday, the Wests Tigers will play the Warriors and Brisbane will host St George Illawarra next weekend.

North Queensland winger Ash Graham was put on report in the seventh minute for a high shot on Manly centre Steve Matai, while interchange forward Cory Paterson was stretched from the field with a suspected cracked vertebrae in the 54th minute.

Manly coach Des Hasler said his side will benefit from the week's rest and will need to improve their first half effort for the bigger matches to come.

"I think there was a good lesson for all of us there in that first half, because the next game is going to be sudden death so we'll take that on board and it gives us two weeks to freshen up and we'll go again," he said.

"It (first half) was uncharacteristic, certainly wasn't the way we intended for it to go but this side's got a lot of character."

Hasler slammed the NRL's decision to hold the match away from Brookvale.

"Yeah disappointing, didn't work from that point of view," Hasler said.

"If Manly are playing North Queensland it's not a hard one is it to work out? We would have easy got 20,000 (at Brookvale).

"So 13,000 it's probably 10,000, there's probably a bit of fudging there I don't know, but clearly there's a lesson there ... we all make mistakes."

However, despite the small crowd, NRL chief executive David Gallop defended the reasons for playing the game at the SFS.

"The decision re the home finals was agreed by all clubs because you couldn't have a situation where higher drawing Sydney teams were penalised and the lower drawing teams retained the home venue," Gallop said.

Cowboys coach Neil Henry was offering no excuses for his team's collapse.

"We were in the game the first 40, we played some very good footy but seven unanswered tries, it's pretty hard to discuss how it happened," Henry said.

"It was pretty comprehensive in the end which is disappointing.

"They were able to maintain their focus for 80 minutes and we weren't.

"That blow out at the end, it's a nightmare really.

"We expected to win, we didn't come here hoping to win."

Cowboys captain Thurston said he was "devastated" and "didn't see it coming at all."

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