The Magpies have now kept alive their hopes of a third consecutive Grand Final berth, after winning 10.13 (73) to 9.6 (60).
Collingwood will take on the Swans on Friday night at ANZ Stadium and should take significant confidence into the meeting, given it has beaten the Swans the last 11 times the sides have met (including seven games at ANZ Stadium.)
It ended an emotional week for the Magpies, who were clearly affected by the tragic death of Port Adelaide midfielder, and former Collingwood player, John McCarthy.
The Eagles rocketed to an early 23-point lead but were slowly pegged back, before Thomas played a starring role after half-time.
Thomas, who admitted he had a "shocker" in last week's Qualifying Final loss to Hawthorn, was back at his infectious best. He kicked three goals in seven minutes and turned the game in Collingwood's favour before the last change.
Many expected the Magpies to overrun the visitors in the final term. The Eagles had managed only one goal for the third quarter, like the second, and seemed out of legs. However, this game had one more twist, with the Eagles kicking three consecutive goals and regaining the lead at the start of the last term.
But after coming this far, the Magpies weren't about to stop.
Tyson Goldsack made the most of a West Coast turnover to kick the Magpies back in front, before a cool, calm and collected Dane Swan snapped a goal around his body for the final goal of the game.
Central to the win was Scott Pendlebury, the Magpies' acting captain and the best player on the ground. He had 29 disposals and they were all classy, finding space in a tight game, thinking clearly when others couldn't.
Dayne Beams (30 disposals), Steele Sidebottom (25) and clever forward Goldsack were other strong contributors.
The Eagles were led by midfielders at either end of the spectrum: veteran Daniel Kerr with 29 touches, and 20-year-old Andrew Gaff with 26 and unrelenting run.
As is expected in the finals, this was not a game easily won. In fact, early signs suggested it might not be a game won at all by the Magpies.
Although the visitors looked sharper and quicker across the ground, Nathan Buckley's team wasn't helped by a contentious umpiring decision that raised more questions about the AFL's goal-review system.
Midway through the opening term, Eagle Andrew Embley attempted to rush a behind. The ball appeared to cross the line before Goldsack swooped on it and brought it back into play, resulting in Andrew Krakouer snapping what was judged Collingwood's first goal.
Krakouer celebrated and the ball was brought back to the centre square and was about to be bounced before technology was introduced.
Footy's 'third umpire' decided the ball had fully crossed the line, even though the vision seemed inconclusive. Regardless, the goal was awarded, then annulled, and Krakouer's scored was wiped. Doubtless the discussion will continue in the game's aftermath.
Eight goals were kicked in the first quarter, something of a mirage of what was to come. Each side could manage only a goal apiece in the second term, as space was shut down and possessions became harder to win.
Football legend Leigh Matthews, commentating on 3AW, said he was exhausted just watching the game, such was its intensity.
That fanaticism, from both teams, continued in the second half but the Magpies were too good when it mattered.
Even without captain Nick Maxwell, they shut down the Eagles' tall forwards, and closed down important defender Shannon Hurn, who had only 14 touches and minimal impact. It was a night where plans were implemented and executed by the Magpies.
And, in six days, they'll have to do it all again.
COLLINGWOOD 3.4 4.5 8.10 10.13 (73)
WEST COAST 5.1 6.4 7.6 9.6 (60)
GOALS
Collingwood: Thomas 3, Swan 2, O'Brien, Pendlebury, Jolly, Blair, Goldsack
West Coast: Hill 2, Darling 2, Kennedy, McGinnity, Kerr, Cox, Naitanui
BEST
Collingwood: Reid, Jolly, Pendlebury, Thomas, Swan, Johnson, Toovey
West Coast: Gaff, Kerr, Cox, Glass, Mackenzie, Priddis
INJURIES
Collingwood: Dawes (leg) West Coast: Nil
SUBSTITUTES
Collingwood: Alan Didak replaced by Jamie Elliott at the start of the last quarter
West Coast: Quinten Lynch replaced by Matt Rosa in the third quarter
Reports: Nil
Umpires: Rosebury, Stevic, Schmitt
Official crowd: 65,483 at the MCG
