The Belgian, who won Milan-San Remo and Strade Bianche on the two previous weekends, was led to the final few hundred metres by his Jumbo-Visma team in a final kilometre that featured a short descent ahead of a sharp incline up to the finish line.
The in-form rider managed to hold off Daryl Impey (Mitchelton-Scott), with Egan Bernal (Team Ineos) sprinting to third, taking four bonus seconds over the rest of his general classification rivals.
"Apparently I have good legs," said Van Aert, "I came really tired to the hotel yesterday, after a few days off. The team still wanted to do a perfect job for me today because we saw some chances in the stage. When you have riders like Tony Martin and all these strong leaders that pulled for me in the end, I had so much motivation to go all-out in the sprint.
"I told the guys I was feeling good and wanted to give it a go. When we started to go uphill I had a whole yellow train in front. Primoz, Tom, and Steven are the leaders for us here but they still helped me. This is a big team victory, and we keep the momentum."
Jumbo-Visma took control of the race from the start, committing to putting Tony Martin on the front in the early stages to control the early breakaway of Brent van Moer (Lotto Soudal), Niccolò Bonifazio (Total Direct Energie), Michael Schär (CCC Team), Quinten Hermans (Circus-Wanty Gobert) and Tom-Jelte Slagter (B&B Hotels-Vital Concept).
The break was never allowed more than five minutes advantage on the peloton and a crash for Hermans and van Moer meant that the front group was under strength and eventually reduced to just Schär forging a lone path at the head of the race.
Soren Kragh Andersen (Sunweb) and Remi Cavagna (Deceuninck-QuickStep) went on the attack from the chasing peloton, and they were soon joined by Quentin Pacher (B&B Hotels-Vital Concept). Pacher took more risks on the 15km descent to catch Schär, but pushed his luck too far when he slipped out on a right-hand bend.
Cavagna and Andersen then caught Schär before Cavagna attacked solo, but it was all just marking off the kilometres until the sprint finish with Robert Gesink (Jumbo-Visma) setting a hard pace over the hills and valleys leading to the finale.
Rigoberto Uran (EF Education First) took a flyer within the final two kilometres to try and steal a march before the sprint, but he was tracked down by the other general classification candidates before the Jumbo-Visma train delivered van Aert to the line.
Daryl Impey made a valiant attempt to come from a few places back and challenge the Belgian star, but couldn't quite make it, with Bernal in an impressive showing for third.
The most notable absence from the front group was Chris Froome, who dropped off the peloton with six kilometres remaining and finished five minutes and 23 seconds down, but was chatting with teammate Jonathan Castroviejo at the time and didn't appear to be in much difficulty.
Richie Porte was the top Australian finisher in 28th, on the same time as the front group.
Van Aert will wear the yellow jersey into the second stage, which concludes with a summit finish on the Col de Porte.
You can watch the Criterium du Dauphine live and free on SBS VICELAND with Stage 2 starting from 10.45 AEST.