Sergent (Radioshack Nissan Trek) started strongly to be 18th through the first split at 14kms before edging back to 26th at the midway point.
The Feilding rider finished strongly in 1:02.04.65.
Bewley (Orica GreenEdge) also started powerfully to be 19th fastest at the 14km split but 28th at halfway before slipping three more places in the final hilly finish of this gruelling test.
There is a day off tomorrow before the action moves to the road with Alexandra's Sophie Williamson the sole New Zealander in the junior women over five laps (80kms) of a similarly challenging course that includes 10 climbs.
The under-23 men (Tom David, Josh Atkins, and Tom Scully) and elite women (Linda Villumsen, Emily Collins, Emma Crum, Kate Chilcott) compete on Sunday (NZ time) with the elite men (Jack Bauer, Julian Dean and Hayden Roulston) racing on Monday.
Results: Individual time trial, 45.7km, elite men: Tony Martin (GER) 58:38.76, 1; Taylor Phinney (USA) 58:44.13, 2; Vasil Kiryienka (BLR) 1:00.23.75, 3. Also: Jesse Sergent 1:02.04.65, 23; Sam Bewley 1:02.37.92, 31.