It proved an outstanding return to international track competition for the 23-year-old Scully, who won a World Cup in Melbourne four years ago but had his career thwarted after a serious accident when racing on the roads in Ireland.
Scully was contesting a sprint for the New Zealand team at the RAS Tour of Ireland in 2010 when he crashed into a lamp-post.
The UK-based professional road rider, who took a year to recover from the effects of his crash, made his return to the track in the Oceania Championships on his home velodrome of Invercargill late last year.
He also finished runner-up in the Points race in Guadalajara, only two points behind the winner, after being one of four riders to put a lap on the field.
Bevin, 22, has been based in the US for the past four years riding for pro Continental team Bissell Racing, before returning to New Zealand fulltime late last year and turning his attentions back to the track.
The pair led early until the Belgian combination won the penultimate sprint to draw level on points but the Kiwis answered by winning the final sprint to claim the honours.
National coach Dayle Cheatley was thrilled with the performance.
"We sent them over to do a job and they did the job - you can't ask for anything better."
Scully has a clause in his professional contract which allows his release should he make the team for Glasgow this year. His chances must surely have been boosted by his latest performance.
The other podium went to Auckland's Sam Webster who beat fellow BikeNZ rider Eddie Dawkins for the bronze medal in the men's sprint.
Earlier Dawkins was the third fastest qualifier in 9.912 seconds, with all three New Zealand sprinters going under the 10-second barrier.
In other racing, world championship medallist Simon van Velthooven was fourth in the men's 1000m time trial in 1.00.214s, won by Australian Scott Sunderland in 59.675, and won the ride-off for seventh to 12th in the keirin after finishing fourth in the semifinals.
The men's team sprint could only manage sixth place with a solid 43.860s effort.
Bevin was 10th in the 4000m individual pursuit in 4:31.519 while the development squad was 10th fastest in the 4000m team pursuit in 4:09.209.
The squad returns to New Zealand ahead of team selections for the UCI World Championships starting in five weeks.
