The Jumbo-Visma rider triumphed after a very sedate day of racing from Gap to Privas, with no breakaway to set the pace.
Van Aert closely followed the Sunweb lead-out train and pursued their sprinter Cees Bol into the final turn, powering past the Dutchman to secure his first victory of this Tour.
Speaking to Eurosport after the stage, the former cyclocross world champion said: “It was maybe the most easy stage I ever did in a cycling race because there was no breakaway, not a high pace at all but then everyone was fresh and the last hour was really hectic and there was a lot of wind.
“The sprinters and the GC teams wanted to be at the front then the last kilometre was slightly uphill, so I knew this stage suited me and i’m just so happy I got the opportunity from the team to go for it.
“When you have a shot and you can finish it off it’s even more sweet.”
Van Aert made the overnight switch from mountain domestique to sprinter for stage five, having put in a huge turn on the final climb to Orcières-Merlette the previous day and setting up his team-mate Primož Roglič for the stage win.
But Jumbo opted to give Van Aert his own opportunity for victory on a stage with a slight uphill in the final kilometre.
On taking up the sprint after his support duties, Van Aert said: “I had a lot of time to recover because the beginning was quite easy. I
“If the shape is good you recover quite well. The team is going strong and we just need to keep this fight. I have my stage win now and from now on I will support the team even harder than I did before.”
He added: “It was quite important to keep the position. It was a hard uphill I managed to be behind Sunweb, who did a good lead-out. I launched my sprint from the moment I saw Bol going in front of me. It was quite tight. I was on the outside and I think it was half a wheel, but it was enough.
“With a lot of happiness. Our leader showed his strong legs yesterday and tomorrow is another important stage.”