Led by five goals to Travis Cloke and superb performances from midfielders Dayne Beams and Dane Swan, the Magpies absorbed blows and landed the most telling to eventually run out 12.13 (85) to 12.10 (82) winners.
It is the Magpies' ninth successive win.
Collingwood led by eight points at quarter-time, West Coast took a six-point lead to halftime.
The Magpies then exploded in the third term, booting the first five goals of the quarter - two to Cloke - as Swan and Beams shared the ball to the exclusion of others.
They had 22 possessions between them in the quarter and the Magpies a 27-point lead.
But just as Collingwood appeared to be rolling, the Eagles fought back.
Two goals late in the third quarter and the opening majors of the fourth to Jack Darling, Nic Naitanui and Josh Hill gave West Coast back the lead.
With control of the clearances and suffocating tackling pressure, the Eagles then looked the more likely.
But the outstanding Beams won a free-kick, then booted truly from a sharp angle on the left for his third goal to give Collingwood a two-point lead with seven minutes remaining.
It proved the match-winner amid the even more breathless footy which followed - Collingwood booting a couple of behinds and the Eagles spending the last two minutes of the match camped in the Magpies' 50-metre arc.
Yet the Magpies stood up defensively to deny the Eagles an opportunity to score, and eventually ran out winners.
Beams finished with 34 touches to go with his three goals, while Swan ran riot with 38 possessions.
Daniel Kerr and Beau Waters were the Eagles' best, while Quinten Lynch booted two goals in his 200th AFL match.
The Magpies now have a 10-2 win-loss record and sit top of the table, with the Eagles 9-3.