And then later in the day, Katusha's Rick Zabel timed his sprint finish to perfection to claim victory in the second stage of the men's race.
Boy van Poppel (Roompot-Charles) finished second ahead of a trio of British riders; with Chris Lawless (Team Ineos), Andrew Tennant (Canyon dhb) and Daniel McLay (Great Britain).
Stage one winner Jesper Asselman retains the leader's jersey.
In the women's race, 20-year-old Wiebes sprinted to victory in front of thousands of fans after a breakaway consisting of Sheffield's Lizzie Banks for the Bigla team, was caught with 3km to go.
Otley's Lizzie Deignan, the former world champion and Tour de Yorkshire winner, finished in the bunch after twice driving the peloton in pursuit of the break.
But the Trek-Segafredo rider, in just her third week back racing competitively after the birth of her daughter last September, was unable to keep pace with the leadout.
Victory was claimed by Wiebes thanks to a strong performance from her Parkhotel team.
"It's one of the best wins of my career," said the young Dutch rider.
"When the breakaway was caught I thought I can win this, and the team did an amazing job to put me in a strong position in the train.
"I looked back and saw I was going to win."
Like all the women's peloton, Wiebes will be hoping to be back in Yorkshire in September, contesting the UCI Road World Championships.
Stage one of the women's race, and stage two of the men's race on Friday, rides part of the finishing Harrogate loop.
"It was a really nice part of the course. It was technical and I like technical."
Deignan, making her first appearance at her home race since winning it in 2017, said: "Phenomenal that they were still all out there in the pouring rain. There were people in shorts and t-shirts, we’re so grateful they were still out supporting us."You never get tired of being in front of a home crowd. I didn’t quite have the legs today to pull anything off but there’s always tomorrow."
Further down the field enjoying a poignant moment as the peloton rode past her home in Bramhope, was Leeds’s Gaby Shaw of Brother Tifosi.“It was as hard as expected. We held our own and stood our ground,” said Shaw. “These girls ride against each other week in, week out, and we don’t have that.“But it was good to get Leah (Dixon) in the break and get the combativity award.”