Van Aert suffered one fall, nearly collided with a Team DSM car and lost virtual grip on the yellow jersey several times during the 153.7-kilometre journey from Lille to Arenberg.
It was a far cry from the 27-year-old's impressive solo attack to take Stage 4 in Calais, though the complicated day was made a little easier by Jumbo-Visma's defence of both his GC lead and Jonas Vingegaard's chances.
"We had big plans today, and definitely this was not what we came for," van Aert said after the stage.
"We were strong as a group, but we could not bring pressure on our rivals and that's a shame. I'm disappointed I could not do more than chase at the end.
"It was just a sh*t day, Jonas had a mechanical and struggled for a bike change, then we lost Primož and I didn't see how that happened.
"We didn't know what happened to Primož, but in 15 minutes so much happened, it was difficult to keep an overview."
Co-leader Primož Roglič wound up losing minutes on all his rivals as Simon Clarke conquered the 11 cobbled-sectors en route to victory, causing van Aert to chase through the fog and preserve his 13-second lead in the GC.
"In the middle of the stage, when I crashed, I thought for sure I was going to lose it, I was so far back and my legs didn't feel good.
"So it was an easy decision to fully commit to teamwork. I had to work to try to bring [Tadej] Pogačar [UAE Emirates] back, but I had no clear overview. So I stayed with Jonas to try and minimise the gaps.
"I think everyone liked it more yesterday but days like today you have to overcome.
"We kept everything good for Jonas on the GC and I'm proud of the way everyone committed in the chase. We will keep fighting."
The display of teamwork from Jumbo-Visma means Vingegaard now sits 40 seconds back ahead of Stage 6, though van Aert remains confident Roglič, too, can impact the GC battle over the next two weeks of racing.
"Of course Primož is a bit far back, and maybe a minute or two feels like a lot, but that can definitely change again," he added.
"First we have to check if Primož is OK, but today has shown for certain we have two of the strongest Tour de France riders in our team."
The Tour de France continues with a hilly Stage 6 over 219.9 kilometres from Binche to Longwy. Watch it LIVE tonight on SBS, SBS On Demand and the SBS ŠKODA Tour Tracker.
