Pogacar wins joint-record third Tour of Flanders
Van der Poel was himself aiming for a new record fourth victory in the second Monument of the season, but instead, Pogacar made it two from two in the prestigious one-day classics having won Milan-San Remo last month.
Pogacar, 27, now has 12 Monument victories, putting him clear in second in the all-time list behind only the great Eddy Merckx with 19.
He has raced three times this year, winning all three and if he wins Paris-Roubaix next weekend, he will join an elite band as just the fourth man to win all five Monuments after Merckx and fellow Belgians Rik Van Looy and Roger De Vlaeminck.
"It was a really crazy race today, I don't know what to say: super-hard from I don't know which kilometre," Pogacar told Belgian TV.
"I don't race too much, so when I race there is pressure to win.
"So far everything went perfect for me, so I can be more than happy.
"Coming next week to Roubaix, I can go motivated, but I try to enjoy the cobbles."
On his Roubaix debut last year, he finished second to Van der Poel, who won for the third year in a row.
Double Olympic champion Remco Evenepoel, on his Flanders debut, held on for an impressive third place ahead of fellow Belgian Wout van Aert after 278km and more than six hours riding around Flanders, with its punchy climbs and numerous cobbled sections.
Pogacar a cut above
In what was billed as a battle between four of the biggest stars in cycling, Pogacar once again proved he is a cut above the others, although Van der Poel -- one of the greatest cobbled classics specialists of all time -- pushed him all the way.
Pogacar had dropped all his rivals bar Van der Poel and Evenepoel with an acceleration on the second of three ascents up the Oude Kwaremont climb with 57km to race.
Evenepoel was left behind on the very next climb, the Paterberg, and although he kept within a handful of seconds at first, he would gradually drift backwards, finishing more than a minute after Pogacar.
Pogacar and Van der Poel rode together for the better part of 40km, before the Slovenian put in his race-winning move on the final ride up the Oude Kwaremont.
He crested that with a six-second advantage, but Van der Poel's resistance was broken and he would only lose more time before the finish.
A 13-man break, including Mongolian Sainbayaryn Jambaljamts, escaped in the first 40km and built up a maximum lead of about five-and-a-half minutes, thanks in part to the peloton being held up at a level crossing.
That lead stayed fairly stable for more than 100km before the peloton upped its pace.
With just over 100km left, Pogacar's teammates put the hammer down on the Molenberg climb and caused a split that saw a group of about 15 riders containing the favourites form a chase group.
The favourites caught the breakaway group with just under 80km left to ride, by which time their lead over the peloton had risen over one minute.
From then on, it was a question of whether anyone would be able to stay with Pogacar over the remaining climbs to the finish -- and no one could.