He said he realised he had successfully pulled away with about 5km to go.
"On the downhill, I turned around and I couldn't see anyone."
Bain won the race in a time of 2hr 27min 23sec, 23 seconds ahead of Phipps.
Bain said he was stoked to win the race and the flat course really suited him between Rotorua and Taupo.
There was not a cloud in the sky when racing began near Copthorne Hotel on Saturday morning.
More than 1300 riders took part in the event, which began in Rotorua, went around the back of Reporoa then travelled down Broadlands Rd to Taupo.
Rotorua cyclist Phipps, who was the first local rider home, said he really enjoyed the event. Phipps, 18, cycled alongside Rotorua's Aaron Perry and Reporoa's Pete Smits, who helped get him on the podium.
"It was a pretty easy ride. These two did all the work for me and I didn't really have to do anything."
The young sprinter managed to get himself out in front of a large chasing group, which included 20 elite riders.
The entire chasing group crossed the finish line within a few seconds of each other.
Rotorua's Ben McHale (11th) was another local rider part of the chasing pack.
This year was the first time the Rotorua to Taupo 100k Flyer has featured a separate elite field. About 50 elite riders contested $2000 in prize money, with the winning man and woman both getting $500.
The winning woman this year was Cambridge's Sophie Williamson. She finished ahead of second-placed Racquel Sheath (Cambridge) and third-placed Kerri Anne Page (Hastings).
Other members of the successful Nature Valley team from Auckland included Sam Lindsay, who won the race last year, Steve Furminger and Brad Tilby.
Third place getter and Nature Valley rider Markby said it was especially satisfying to do well on Saturday after being disqualified a few years ago at the same event.
The course will be reversed next year to start in Taupo and end in Rotorua. Last year marked the first time the course was reversed and it will now alternate each year.