Rowney launched a well-timed attack and held off compatriot Annette Edmondson to win stage four of the La Route de France, a 103km race from Autun to Louhans-Chateaurenaud.
Italian Elisa Longo Borghini finished sixth to retain her overall lead.
Rowney has a professional contract with Velocio-SRAM, but is leading the Australian development team for the six-day French tour.
She was sprinting to the finish of the Dutch Drenthe 8 race in March when a fan's arm came out over the barricades and touched her handlebars.
The high-speed crash temporarily sidelined Rowney with a collarbone fracture.
On Thursday (AEST), Rowney timed her solo sprint perfectly with about 600m left.
Team director Donna Rae-Szalinski said every member of the young Australian team deserved credit for the win.
"I looked up from the car at 5km (to go) and I saw the whole team on the front," she told CyclingTips.
"Here's this young development team, and every single rider is on the front of a UCI race in Europe.
"It gave me goosebumps to see that and to think about how far they've come.
"We've had 11 race days in Europe together and they've already pulled off a massive result."
Rowney's team-mate Jenelle Crooks also leads the young rider category and is 11th overall.
But fellow development team member Kimberley Wells crashed in the last 300m.
Lauren Kitchen (Hitec) is the best-placed Australian overall in fourth, 10 seconds behind Longo Borghini, and Carlee Taylor (Lotto Soudal) is seventh at 21 seconds.