Dutch rider Demi Vollering won the race after also taking Sunday's stage with a solo attack.
Vollering began the final stage with an eight-second lead over Niewiadoma-Phinney but did not settle for defending her advantage.
On the final climb, the Col d'Eze, she responded to an attack by the Polish rider and then counterattacked before the summit.
Vollering quickly opened a gap over Niewiadoma-Phinney and extended it over the final kilometres to the finish on Nice's Promenade des Anglais.
Niewiadoma-Phinney was caught by a chasing group on the flat roads into Nice but recovered to finish third in the stage.
Polish national champion Dominika Włodarczyk finished ninth in the stage and maintained her place in the top 10 overall, ending the race seventh.
Niewiadoma-Phinney's second-place overall finish was her first runner-up result in the Tour de France Femmes. She won the race in 2024 and finished third in 2022, 2023 and 2025.
The 31-year-old Pole lives and trains in Andorra. Her training partner and husband since 2024 is former American professional cyclist Taylor Phinney.
(gs)
Source: IAR, PAP, Eurosport