Deignan and Banks made their move away from the peloton with 35 kilometres to go, just after a crash saw a large part of the peloton held up.
Jip van den Bos (Boels Dolmans) initially joined the move, but crashed out of the attack almost immediately, leaving the British pair of riders to go with just each other for company in the wet and windy conditions.
A chase group formed behind, but didn't cooperate well, with just the Mitchelton-Scott pair of Grace Brown and Annemiek van Vleuten consistently forcing the pace of the pursuers.
The gap to the front pair was reduced to 20 seconds at its lowest point with 12 kilometres remaining, but the impetus went out of the move and the lead of the pair in front ballooned out in the final kilometres.
Deignan looked the stronger of the two throughout and after manoeuvering Banks to the front in the final kilometre, she launched her final sprint and was a comfortable winner.
“Obviously I’m delighted, it’s been a difficult season for everybody so far and we’ve had a lot of bad luck in the first few races," said Deignan. "It’s been clear to me that we’ve had the strongest team in all the races and finally the luck was on our side."
The victory is Deignan's third at the race, and ended a dry spell for her Trek-Segafredo team which had been starved of results since the season restart.
"Plouay is a really nice race and I always seem to do well here," said Deignan. "The rain came which was an extra bonus for me, finally no more sweating in the heat for me! I’m really, really happy and grateful to the whole team for their effort."
Elizabeth Banks was the surprise of the race, coming in second behind Deignan, with the peloton led home in the sprint by Chiari Consonni (Valcar-Travel Service).
“I fully committed to the move with Lizzie Deignan because even if it didn’t come off, I knew that I had a number of very strong teammates in the group behind," said Banks. “Those were both great options for us to get a podium. I did not know at this point whether our move would come back, but I wanted to commit to it.
"I knew that in the sprint, I needed to start behind her, but I was not able to get behind her. Of course, Lizzie has won Plouay before, and that was the point where her bigger experience showed. But we worked well together and were well-matched, and I am delighted about coming second, it is a really great result for our Continental team.”