An elite ride on the TT bike from the Belgian saw him clock the fastest time of 16 minutes and 20 seconds on the 13.4 kilometre course in Montluçon, two seconds faster than Primož Roglič and six seconds faster than Australian Rohan Dennis.
While he also took the yellow jersey, it was only off another Jumbo-Visma rider in domestique Christophe Laporte, who had held the overall lead for the first three days of the race after being gifted victory by Roglič and van Aert in the opening stage.
National time trial champion Dennis occupied the hot seat for most of the day after starting early and motored through the course before his superstar teammates set off at the end of the day and put in their own blistering rides.
Many of the race favourites lost time on Jumbo-Visma leader Roglič, with Nairo Quintana (Arkea-Samsic), Adam Yates (INEOS-Grenadiers) and Aleksandr Vlasov (BORA-Hansgrohe) all losing over a minute.
Simon Yates (BikeExchange-Jayco) was able to put in a strong performance to remain closest to the Jumbo trio in fourth overall, 49 seconds back from van Aert. Laporte now sits third, 28 seconds back and Roglič second just 10 seconds behind top spot.
Van Aert revealed following the stage that he was worried he'd be able to surpass Dennis' superb ride after watching it unfold from the team bus, so had to work hard to ensure he did so when he got out on the course.
“Until now it’s been a perfect week. We’ve really attacked this race and shown what we’re here for. Today everyone was motivating each other and it results again in a nice podium,” Van Aert said after the stage.
“Our coach planned the winning time around 17 minutes then Rohan did a 16.25 so in the bus we were worried if we could beat him.
"It was a hard effort to manage because it was always up and down - not one steady rhythm - and for the last steep part you needed something left. I managed to save something on the downhill, making myself as aero as possible, then went full gas on the climbs.”
Now at the halfway point of Paris-Nice in the yellow jersey, van Aert revealed his focus is starting to turn to the upcoming Classics races as he looks to consolidate Jumbo-Visma's lead and only hand the jersey over to teammate Roglič, maybe not even him if the all-rounder is in some special form.
"I hope to wear the jersey as long as Primož doesn’t take it over from me," Van Aert said.
"The hardest stages are coming now, and for me a lot of nice things after. We will start tomorrow and really enjoy this yellow jersey, and then we will see day by day."
"I think the most important part of Paris-Nice is over for me. It’s a race of preparation for me for the classics that are coming, and I hope to hand this jersey over in one of the next days to my teammate Primož, we are here to win with him."
Watch a full replay of Stage 4 of Paris-Nice below:
Paris-Nice continues tonight with the first of the mountain stages, a 189 kilometre journey from Saint-Just-Saint-Rambert to Saint-Sauveur-de-Montagut featuring three category one climbs that's sure to produce fireworks. Catch all the action from 12:15am (AEDT) LIVE on SBS and SBS on Demand.