Corby Price (Hamilton Boys' High School) was second with Westlake Boys High School's Jack Tutill third.
Georgina Wilson (Auckland Diocesan) won in a similar fashion to Saunders with a late and drastic acceleration to win the under-20 women's race over 33kms in 55m:31s.
"I didn't expect to win, but I was quite confident with the way I was sitting throughout the race that I had the potential to win it, but it was a really tough field with some great riders so it was always going to be tough," said Wilson.
"I'm really happy with how I went today; it's a great way to finish off the schools cycling phase of my life."
Second place went to Rangi Ruru Girls' School's Alice Hay, with Devon Hiley from St Cuthbert's College third.
Both senior champions are also accomplished track cyclists with Wilson having recently competed at the Junior Track World Championships in Invercargill while Saunders is gearing up to compete for the BikeNZ team at the Oceania Track Championships in Adelaide in November.
The championships conclude with a points race around the Manfeild Autocourse in Feilding tomorrow.