The 25-year-old Jumbo-Visma rider from Belgium kept his cool in a two-way sprint at the end of the sweltering 305km race to pick up the first Monument of his career – a week after his victory in Strade Bianche, the first WorldTour race following the long interruption brought about by the ongoing coronavirus crisis.
Van Aert's victory over Alaphilippe (Deceuninck-QuickStep) means he emulated the Frenchman's Strade Bianche-Milan-San Remo double from last season.
The race's two out-and-out favourites were untouchable on the Poggio, dominant on the descent, and just held on as the chasing pack surged back into contention, with the Australian Michael Matthews (Team Sunweb) crossing the line two seconds down to take the final place on the podium.
Watch Wout van Aert pip Julian Alaphilippe in thrilling Milan-San Remo finish
There were places in the top five for Slovakia's Peter Sagan (Bora-Hansgrohe) and Italy's Giacomo Nizzolo (NTT Pro Cycling) while Belgium's Philippe Gilbert (Lotto Soudal) settled for ninth place in his quest to add the one remaining victory he needs to complete a grand slam of wins in cycling's five Monuments.
But the day belonged to the man-of-the-moment van Aert, who fought back after an apparent wobble on the Cipressa climb inside the final 40km to take arguably the biggest win of his already illustrious career to date after just over seven hours and 16 minutes in the saddle.
"Of course, I'm super happy," said van Aert after becoming the third rider in history to win Strade Bianche and Milan-San Remo in the same year – after Poland's Michal Kwiatkowski (2017) and Alaphilippe last year. "I can't believe about these two victories in a row. I don't have any words. To start the second part of the season with a victory in a Monument is crazy, really nice."
Wout van Aert delighted with 'incredible' victory at Milan-San Remo
It was Alaphilippe who made the decisive move, the Frenchman battling back from a puncture ahead of the Cipressa to put in a stinging attack which blew the race apart on the Poggio. Only van Aert was able to match his acceleration – although he admitted he had his work cut out.
Hold on, hold on, hold on – that was the only thing in my mind. He went early and I had to close the gap on him. But on the downhill I came back. Julian played it really well and put me on the front. I had to keep the speed because the pack was returning – it was hard to keep something back, but I had just enough to win by half a wheel.
A new-look course for the first Monument of the season took the riders across unfamiliar roads through Piedmont and over two different climbs before the race hit the Ligurian coast in the town of Imperia for the traditional final 40km of breakneck action.
Italians Alessandro Tonelli (Bardiani CSF Faizane), Fabio Mazzucco (Bardiani CSF Faizane), Manuele Boaro (Astana), Mattia Bais (Androni Giocattoli-Sidermec), Damiano Cima (Gazprom-Rusvelo) and Marco Frapporti (Vini Zabu-KTM), and the Spaniard Héctor Carretero (Movistar) attacked on the outskirts of Milan to form the day's break.
The gap peaked just shy of seven minutes as the race tackled the Niella Belbo and Colle di Nava climbs ahead of a technical and twisting decent into Imperia. The veteran Boaro was the last man caught just as the race joined the Mediterranean coast that is the usual shimmering calling card of La Primavera - not before a touch of wheels in the peloton ended the chances of his compatriot Matteo Trentin (CCC Team).
'Oh dear!' - Matteo Trentin suffers nasty crash at Milan-San Remo
Sprinters Caleb Ewan (Lotto Soudal) and Fernando Gaviria (UAE-Team Emirates) wilted in the 30-degree heat on the Cipressa as the tempo was ratcheted up by a series of attacks from the Trek-Segafredo and Circus-Wanty Gobert teams.
Sagan's shaggy-haired teammate Daniel Oss enjoyed a stint on the front after attacking on the descent of the Cipressa – but the rangy Bora rider was swept up ahead of the Poggio with 8km remaining.
With Deceuninck-QuickStep's Irish sprinter Sam Bennett feeling the pinch on the climb, the Irishman's teammate Alaphilippe made his move with an emphatic attack not entirely dissimilar to his winning move from 16 months earlier.
Milan-San Remo highlights - Wout van Aert triumphs in pulsating finish
But Alaphilippe met his match in the supremely talented van Aert, the triple world cyclocross champion proving that he has fully recovered from the terrible injury sustained in his debut Tour de France last summer by sprinting to the first of what could be many Monument wins with the chasing pack breathing down the leading duo's neck.
The second Monument of this topsy-turvy season comes next weekend with Il Lombardia - usually the fifth major classic of the season, brought forward from its usual autumn date to accommodate the re-jigged Grand Tour calendar. After victories in Strade Bianche and Milan-San Remo sandwiching third place in Milano-Torino, his rivals will be glad to know that Wout van Aert will instead be riding the Criterium du Dauphine...