Souths coach Andrew Ryan described it as a "rollercoaster".
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Lions fullback Lachlan Walmsley said he felt "pumped" but also spoke of his "relief" at the full-time whistle.
Having survived that thrilling encounter, Souths will now meet fellow semi-final winners Cessnock at the same venue this weekend.
Souths qualfied for their third grand final in the space of five years (2016, 2018, 2020) and ended Wyong's season in dramatic circumstances. The team in front changed four times in the closing 20 minutes.
"It was a rollercoaster ride," Ryan told the Newcastle Herald.
The Lions shot out to a 16-0 advantage midway through the first half before Wyong opened their account nearing half-time and reduced the gap to 12.
Back-to-back tries after the main break saw the Roos level proceedings before a Josh Mantellato penalty goal put them up by two near the hour mark.
Souths centre Dylan Lucas replied in the 65th minute for a 22-18 lead before Wyong prop Jake Lewis crashed over shortly after to make it 24-22.
Flanagan went over in the south-eastern corner with less than three minutes remaining before Lions halfback Jason Keelan landed the conversion from the sideline.
"It was a bit of relief more than anything," Walmsley said. "It was a great effort to get it done. We were all pretty pumped."
Cessnock coach Todd Edwards said he was "proud" of his squad's efforts, especially having lost halfback Liam Foran (hamstring) and forward Tom Baker (knee) to injury inside the opening 10 minutes.
Foran and Baker, who both didn't return to the field, will now need to assessed this week to see if they play on Sunday.
"Liam is 50-50 at this stage and at a pinch we could have strapped him up and thrown him back out there, but he would have been 100s for this week if we did that," Edwards said. "Tom is going for scans this week so we will just have to wait and see."
Josh Griffiths replaced Foran in the halves in the semi with Josh Charles moving to right centre and Hamish Wolfgang slotting on the wing. Lincoln Smith, who narrowly missed selection, may come into consideration for the decider.
The Goannas piled on 38 unanswered points in almost as many minutes after half-time, having trailled 8-0 at the break. Wests scored a consolation try in the closing stages.
"The second half we really put it together," Edwards said.
"Those injuries didn't help us in the first half, but it was good performance in that back 40 [minutes]. I think we won it in the first half with our defensive resolve. The game could have been gone but that kept us in it."
Griffiths crossed twice for Cessnock while Ngangarra Barker, Harvey Neville, Brayden Musgrove and Harrison Spruce also made the scoresheet.
Wests welcomed back 2017 player of the year and 2019 player of the final Ryan Walker, who had been sidelined for seven weeks after suffering multiple facial fractures in a tackle.
The Rosellas won last year's premiership over Cessnock, who have appeared in six of the previous 12 title showdowns (2008, 2009, 2010, 2012, 2014, 2019).
GRAND FINAL: Cessnock v Souths at Maitland Sportsground on Sunday, October 18 (3:15pm).
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