Longo Borghini responded first, followed by Niewiadoma with Deignan on her wheel, but the Brit says a parked motorbike and ‘one big traffic mess’ hampered her progress.
It left the 25-year-old Italian to claim victory – her first of the season – while 22-year-old Niewiadoma finished two second back in second.
Deignan was a further three seconds back – her best individual result on the Women’s WorldTour since winning the Aviva Women’s Tour in June last year.
But she admitted a tinge of regret that she lost the tactical battle at the end, despite the surprise result.
“Today felt different than usual,” she concluded. “Normally I feel very strong and dominant.
“Today it was much more down to tactics because I didn’t have the legs to animate it the way I’d normally like to. I had to play the tactic game, and I got it wrong.”
UCI Women’s WorldTour – Stade Bianche 2017: result
1) Elisa Longo Borgini (ITA) – Wiggle-High5 – 3.44.45hrs
2) Katarzuna Niewiadoma (POL) – WM3 Energie +2”
3) Lizzie Deignan (GBR) – Boels-Dolmans +5”
4) Lucinda Brand (NED) – Team Sunweb +8”
5) Annemiek van Vleuten (NED) – Orica-Scott +9”
6) Shara Gillow (AUS) – FDJ Nouvelle Aquitaine Futuroscope +12”
7) Katrin Garfoot (AUS) – Orica-Scott +18”
8) Amanda Spratt (AUS) – Orica-Scott +36”
9) Cecilie Uttrup Ludwig (DEN) – Cervelo-Bigla +1.06
10) Elena Cecchini (ITA) – Canyon-SRAM – ST