The GreenEdge rider clocked a time of eight minutes 15 seconds in the 6.8km stage 2B of the race, to claim the leader's jersey.
SaxoBank's Manuele Boaro had looked like winning with a time of 8:23 set earlier in the afternoon, a time later equalled by Nelson Oliveira (Radioshack) and Jonathan Castroviejo (Movistar), but the Australian Under-23 world time trial champion came through late on to win.
Boaro and Radioshack's Nelson Oliveira (Radioshack) are both eight seconds behind Durbridge in the general classification going into Thursday's penultimate stage.
Sacha Modoloa (Colnago), who had led after Wednesday morning's 88km stage 2A, is in fourth place a further four seconds behind.
