Radioshack-Leopard's Swiss star claimed his second triumph in the race after dropping race favourite Peter Sagan on the Paterberg, the 17th and final climb on the arduous 256.2km route.
The quadruple world time trial champion then rode solo to the line, matching his victory from 2010. He finished 86 seconds ahead of the Slovak with Belgium's Juergen Roelandts taking third.
“This was an amazing team job," Cancellara said afterwards. "Everyone was against us and we just stayed focused. We came on the Oude Kwaremont for the last time and Gregy Rast said everyone looked tired, so I tried to do the first selection there. Peter (Sagan) and I came up to Roelandts then and I knew I had to go again to get away from Peter.
"It happened like we’ve been planning for months. Hard work from me and the team and sacrificing time with our families. I can count on two hands the number of days I’ve been home this winter. It hasn’t been easy for my wife and kids but these are the hard choices we make. My career won’t last forever so it’s important to pick moments to enjoy."
The rider known as Spartacus will now look to add a third Paris-Roubaix title to his collection next Sunday with defending champion Tom Boonen a big doubt after crashing out and injuring his hip after just 19km.
Boonen was aiming to become the first rider to win Ronde van Vlaanderen four times but crashed alone and suffered a bruise on his left hip, a wound on his left elbow and on his right knee. He left in an ambulance but x-rays showed that the Omega Pharma Quick Step leader had suffered no fractures.
The crash of the Belgian favourite was the main early talking point with the race taking a long time to come to life.
Andre Greipel attacked on the fourth climb of the day, the Molenberg, and he established a lead group with Michal Kwiatkowski, Maarten Tjallingii, Marcel Sieberg and Laurens De Vrees.
Mirko Selvaggi and Sébastien Minard bridged the gap and those seven men held a small advantage entering the pivotal final 40km.
Kwiatkowski and Selvaggi pushed on after the second ascent of the crucial Oude Kwaremont and Paterberg climbs, which come in quick succession, while behind them Roelandts was one of five men to counter attack out of the peloton.
Sébastien Hinault followed the Belgian and they led the race entering the final 20km.
Lotto-Belisol's Roelandts had another dig on the third ascent of the cobbled Oude Kwaremont but behind him came the pivotal moment as Cancellara made his move and only Sagan could follow.
Roelandts was caught by Cancellara and Cannondale's Sagan ahead of the Paterberg. But the Slovak, who claimed the biggest one-day victory of his career in Gent-Wevelgem last Sunday, could not match the pace set by the Swiss on the climb which has ramps of 20 per cent.
That left a 13.3km time trial to the line for Cancellara who showed no sign of relenting as he gradually increased his lead to over a minute, allowing him time to celebrate a famous victory in front of massive crowds in Aankomst.
Behind Sagan comfortably beat Roelandts in the sprint for second, the 23-year-old matching his position in the year's opening Monument race, Milan - San Remo.
Alexander Kristoff led the whittled-down main bunch over the line, a further 10 seconds back, ahead of Matthieu Ladagnous, Heinrich Haussler, Greg Van Avermaet, Sébastien Turgot, John Degenkolb and Sebastian Langeveld.