Fellow Australian Nick Schultz (Mitchelton-Scott) finished second, with Michael Valgren (NTT Pro Cycling) rounding out the podium. Will Clarke (Trek-Segafredo) led into the final straight, but the Tasmanian was swamped from behind and ended up finishing fourth.
With two riders in the front group, NTT extended their lead at the top of the general classification, keeping the yellow jersey through to final two stages of racing next weekend.
Ovett, who was second in Stage 2 of the Tour de France Virtual, rode an aggressive race, attacking on the ascent of the main climb of the circuit. Ovett's aggression thinned down the group significantly, and while some riders rejoined, Ovett was the freshest at the finish and took out the small group sprint.
“It means a lot," said Ovett. "Everyone knows I enjoy Zwifting and I was close last weekend."
“This is probably my last Zwift race for a while. I’ve got to go back out onto the roads and do some real racing, so no more power-ups and back to reality.”
Ovett also took issue with EF Education First team boss Jonothan Vaughters, who described online racing as more similar to running than on-road racing.
"Looking at the power profiles from virtual TdF today. These races do not mimic on road races, or physiological requirements of on road races, at all. Totally different beast," Vaughters wrote on Twitter.
"I’m hardly taking a swing at Zwift. I’m just fascinated by the profound differences in physiological demands between virtual racing and on-road racing. Virtual bike racing is more similar to running, physiologically, than on road bike racing."
Ovett was himself a middle-distance runner before turning to cycling, currently riding for Israel Start-Up Nation's feeder team.
"I don’t know what Jonathan Vaughters’ history is with running but I don’t think it’s very in-depth, to be honest. Running is completely different, so I don’t know what he’s on about there," Ovett said in the winner’s press conference.
"With running, a lot of people seem to think there are no tactics involved, but if you’ve ever seen someone lead the 10,000 metres or 1,500 metres from start to finish, you’re probably watching the under-8s at a school race."
In the overall standings, NTT Pro Cycling extended their lead to a significant advantage of 75 points. Rally Cycling moved up into second place on 188 points, with Trek-Segafredo now third on 162.
In the women's race Australian Sarah Gigante (TIBCO-SVB) was one of the main protagonists, trying in a similar vein to Ovett to split the race up on the climb. The tactic had limited success, but Gigante contested the reduced bunch sprint and finished fourth.
The win was taken by a late burst from April Tacey (Drops), who took her second stage win of the event, moving her team up to second behind TIBCO-SVB on the standings.
"Coming through the end I used an aero boost," said Tacey. "I was just four seconds off the back over the top of the last climb, with a group of four or five riders. I got back on with 1.5km to go. The aero boost gives you 15 seconds. You have to try and not go too early. I try to be a little bit after (my competitors) go and then use mine so that I have a last little kick toward the finish line."
The Tour de France Virtual concludes next weekend with a stage to the summit of Mont Ventoux on Saturday followed by the traditional finale on the Champs Elysees. Both stages will be broadcast LIVE on SBS VICELAND, starting at 11pm AEST.