Wiebes launched her own sprint on the finishing straight to Gloucester and held off both Alexandra Manly (Team BikeExchange-Jayco) and Coryn Labecki (Jumbo-Visma) to the line.
The Team DSM sprinter had been dropped earlier in the 107.9 kilometre stage, but was able to rejoin a front group lacking cohesion after Canyon-SRAM and SD Worx fractured the peloton on the second climb of the day.
Riejanne Markus (Jumbo-Visma), Christine Majerus (DS Worx) and Gladys Verhulst (Le Col-Wahoo) had formed a three-rider breakaway after Worral Hill, the first QOM of the day, and led the peloton by 45 seconds at the start of the Speech House climb.
It was on this climb that their advantage was reduced, before a group of 17 riders emerged from a peloton permanently fractured by the work of Katarzyna Niewiadoma (Canyon-SRAM), Ashleigh Moolman-Pasio (SD Worx), Elisa Longo Borghini (Trek-Segafredo), Kristen Faulkner (BikeExchange-Jayco), Elise Chabbey (Canyon-SRAM), and Veronica Ewers (EF Education-TIBCO-SVB).
The group, containing the likes of Grace Brown (FDJ Nouvelle-Aquitaine Futuroscope) and Sara Martin (Movistar Team), held a 22-second lead over the next group, with Chabbey claiming the second intermediate sprint.
With less than 10 kilometres remaining, however, the second group was able to bridge the gap with Wiebes now firmly in the mix.
BikeExchange-Jayco and Team DSM had moved to the front of the race as the finish line approached, with Wiebes then moving clear of Manly to take both the victory and yellow jersey after holder Clara Copponi (FDJ Nouvelle-Aquitaine Futuroscope) failed to finish with the first peloton.
"Megan (Jastrab) did a really strong effort to bring me back to the lead group," Wiebes said after the race.
"In the last five kilometres, Pfeiffer (Georgi) and Megan came back to the front and did a great lead-out, and I am really happy to finish it off for them.
"I'm proud of the girls and all the work they did today. We will go all-in tomorrow to try to make it three."
Wiebes' second consecutive sprint victory means she now holds a 13-second lead over Sofia Bertizzolo (UAE Team ADQ) and Manly in the general classification, with two hard stages in Wales still to come.
The Women's Tour continues tonight via SBS On Demand with coverage of Stage 4 commencing at 11:30pm (AEST).
