After a goalless first half, goals from Laura Garside and Chantelle Gallagher secured the points for the visitors, who moved to the top of the table.
Despite the defeat, it was a much improved performance from Rovers, who gave full debuts to Centre of Excellence graduates Helen Seed and Zara Musker.
In a fiercely-contested first half, Nichol Forster saw a shot tipped away from the top corner, before the hosts had penalty appeals for handball waved away.
Stoke were a threat from set-plays and rattled the crossbar before the break.
Rovers were denied by the woodwork themselves straight after the interval and had a couple of chances on the rebound, but couldn’t convert.
The missed chances proved costly as Garside gave the visitors the lead 20 minutes from time after Rovers failed to clear a ball into the box.
Rovers responded well and pushed hard for an equaliser, but Stoke secured the spoils late on through Gallagher’s fantastic free-kick.
Manager John Prince said: “Naturally we are disappointed to lose, but we take satisfaction from how we played and it was great to see two 17-year-olds make their debuts in the back four. Helen Seed in particular showed great strength, composure and positional play for someone of her age.
“We now need to build on the work rate and character that we showed and take our chances when they come along.”
ROVERS: Hutcheson, McLellan (Adams 81), Middleton, Seed, Musker, Young, Flynn, H. Forster, Anderton, Savage (R. Hardy 59), N. Forster (Marsh 57).