The visitors made a terrific start, scoring two tries from turnovers to lead 12-0.
One was a 90m effort that left the home team a bit stunned.
But Waitaki Boys' rallied and tended to dominate from that point.
Arguably, the turning point came when it was reduced to 14 men. Halfback Thomas Hutton was yellow carded for stomping 23 minutes into the match but it was Waitaki that played like it had the extra player.
The home side scored two tries while Hutton watched from the bin.
Prop Tonga Malafu was a standout player, scoring two tries, while fullback Daniel Halaholo was also impressive.
Waitaki led 17-12 at the break and pulled away to win by a comfortable margin, outscoring Dunstan six tries to three.
It was good result for Waitaki, which suffered a 32-13 loss to King's High School earlier in the week.
King's, meanwhile, looks the team to beat. It notched its fourth consecutive win with a comfortable 54-7 win against Mount Aspiring College at the Wanaka Showgrounds.
John McGlashan College is the only other unbeaten side in the competition. It did not have to play this weekend, though, as Kavanagh College was forced to default.
Kavanagh will decide today whether it will front for this weekend's fixture against Taieri College.
In the other games, St Kevin's College beat Taieri College 43-20 in Oamaru and Otago Boys' High School 2nd XV beat South Otago High School 22-16 in a close game at Bishopscourt.
