The 36-year-old set a time of 1:04.480, over four seconds quicker than Jozef Metelka in second.
Neil Fachie and pilot Craig MacLean added tandem sprint gold to their kilo win to complete a successful competition in Wales for the duo.
They defeated Netherlands pair Tristan Bangma and Yorick Bos in the final after qualifying fastest and making serene progress through the quarter and semi-finals.
More medals came with silver for Megan Giglia in the C3 pursuit, along with bronze medals for Lora Turnham and Lauryn Therin in the tandem pursuit, Liz Saul in the C4-5 pursuit, Sally Hurst in the C2 pursuit and Jon Gildea in the scratch race.
The Great Britain Cycling Team end the three-day meeting with six gold, four silver and eight bronze medals as well as important Rio Paralympic qualification points.
The focus will now shift to March’s UCI Para-cycling World Championships in Apeldoorn, Netherlands.
“That time has taken me by surprise,” said Cundy, who had suffered a fitness setback in November, spending a week in hospital.
“I’ve not tapered for this event…and to come out and do half-a-second (improved) PB at sea level – completely gobsmacked.”
Fachie, a double world and Commonwealth champion, is happy with him and MacLean’s position eight weeks out from the world championships.
“When you haven’t raced for a while there is always that slight unknown,” he said.
“Training has been going well but you don’t know what everyone else has been doing, until you get that last few percent of a race day then you’re not sure.
“This has certainly been nice. We’ve probably raced against some of our toughest opponents that will be out at the world champs.
“At this stage they’ve got work to do rather than us but that doesn’t mean we’re not going to keep improving either.”
The UCI Para-cycling Track World Championships take place from 26-29 March.