The 21-year-old has form in time trials, having won this year's prologue at the Criterium Dauphine, and the Circuit Sarthe.
And the 2009 junior world champion finished nine seconds clear of his nearest opponent on the 22.1km route.
French hope Jeremy Roy finished second, nine seconds behind Durbridge's time of 26 minutes, 30 seconds. A further eight seconds back was Lazlo Bodrogi of Italy.
Durbridge's lead in the general classification continues a strong run for his Orica-GreenEdge team in France, with team-mate Aidis Kruopis having won the first two stages in sprints and held the lead himself.
Radioshack's Giacomo Nizzolo had earlier won the morning stage at the Tour du Poitou-Charentes.
The young Italian retained his good form from the Tour de Wallonie and Eneco Tour and out-sprinted Denis Flahaut and Maxime le Montagner to the line, taking his fourth victory of the season.
Nizzolo said afterward: "I'm happy to see that my shape is staying on a high level.
"Yesterday I was angry with how I rode the sprint. Today, the team was determined to help me win and they did great."
Radioshack Nissan Trek general manager Dirk Demol added: "Giacomo was really motivated to do something today.
"We have been sitting back a bit in the first two days, because our big goal is Plouay on Sunday, but last night Giacomo asked me to set up a train for him.
"At 20km to go, the break was still out there and they worked really hard. At one point, the race radio said 'RadioShack au complet en tête': RadioShack complete at the front'. That's nice to hear."
Stage three, at a total distance of 99.4km, was between Pleumartin and La Roche Posay. A break of four riders went early on, but was caught after 60km. Straight after, a threesome tried again and they were caught with 6km to go.
The race concludes on Friday with a final 188.8km stage between Melle and Poitiers which is likely to end in a sprint.