Jeff Hare's two-run home run in the fifth inning was the difference, breaking 1-1 tie.
The Tomcats added a run in the sixth inning, on an Eric Pettipiece RBI single, driving in Riley Garinger.
Alex Pettipiece and Nick Brooks had back to back singles in the fourth inning, setting up a run scored by Alex when Garinger reached based on an error.
Kitchener's lone run came from a Hiller solo shot in the fourth inning.
Eric Pettipiece finished with a single and one base on balls.
Ambrogio worked the first four innings, earning the win, with Newell tossing the fifth to seventh innings.
The Tomcats, 6-2 in league action, visit Brantford Thursday.
Starting Friday, St. Thomas hosts the Ontario Baseball Association 22U provincial tournament this coming weekend.
The Tomcats face Newmarket in their opening game, Friday, 5:30 p.m. at Emslie.