The Belgian Visma-Lease a Bike rider edged Mathias Vacek and Pau Miquel with an explosive burst to the finish line in Cordoba at the end of a 180.5 kilometre ride from Archidona.
Ben O'Connor retains a commanding overall lead after his remarkable stage six victory on Thursday but three-time winner Primoz Roglic snatched back six bonus seconds at the top of the day's only categorised climb.
Van Aert had team-mate and last year's Vuelta winner Sepp Kuss to thank for pulling hard to bring the front of the race together, giving him the platform to snatch victory.
"I knew the final climb was hard but I didn't expect the race would explode like this," Van Aert told Eurosport.
"I found myself with Sepp alone in the front group, it was really difficult to manage but Sepp did such an amazing job.
"The defending champion of this race pulling for you, that's a huge example of our team philosophy -- because of that I'm so proud."
Van Aert had not tasted victory since February but after holding off Kaden Groves in stage three, secured his second triumph in five days in baking Andalusian heat.
Australian O'Connor leads the overall standings by four minutes 45 seconds from veteran Slovenian rider Roglic, with Portugal's Joao Almeida third, a further 14 seconds back.
'Explosive' finale
It was Decathlon-AG2R La Mondiale rider O'Connor's first day wearing a Grand Tour leader's jersey but will not be his last.
"It was a super easy day until the finale, which was explosive," said O'Connor.
"I can't really do much with Primoz's sprint for the bonuses but he'll have to take a lot of bonuses to make up that kind of time."
Xabier Isasa made an early break and kept building on it, moving eight minutes clear of a slow-paced peloton after 50km.
The Spaniard won the intermediate sprint before being swallowed up with 38km to go, as the peloton headed for the Alto del 14 Percent.
Roglic claimed his bonus seconds at the summit, while sprinter Groves crashed at the top shortly afterwards.
The Australian got back on his bike but it kept him out of contention for another sprint showdown with Van Aert.
Marc Soler attacked with 20km to go and carved out a small lead on the chase group which he maintained well.
Van Aert attacked but Soler's team-mate Pavel Sivakov reeled him back in, before the Spaniard was eventually caught with little over three kilometres remaining after impressive work from Kuss.
"The pace was hard but when I saw Wout there I knew he was on a good day," explained Kuss.
"It was a suffer-fest to pull Soler back but it feels like a victory for me too, it was really nice to be there with Wout."
Stage eight of La Vuelta takes riders 159km from Ubeda to Cazorla on Saturday.
