In came Hayden Cargo and Jake Bezzant, who calmly got the innings back on track once Thomas had exhausted his allotted overs for the impressive return of 4/22.
Their partnership moved the score swiftly along to 161/5 before another pair of strikes brought the Bay right back into the contest.
Part-timer Cam Neal removed Bezzant for 39 before the Mount duo of Chris Atkinson and Hayden Byrnes combined for a stumping to uproot Cargo.
That left the Hamilton side needing 25 runs from the final five overs with three wickets in hand, setting up a tense finish.
The Bay side had posted 190/7 in the first innings thanks to a fine rearguard action by Thomas and Atkinson.
The pair put on 64 in an unbeaten eighth wicket partnership that gave their side a sniff after being reduced to 126/7.
Thomas, who rarely bats for his club side, exhibited a solid technique before opening his shoulders to club a rare six to provide the highlight of the innings.
Earlier, poor running and a gradual loss of wickets pinned down the home side's batsmen.
Kent Hodder and Hayden Byrnes were both caught short of their ground inside the first nine overs, before Myles Timoti's cautious knock ended on nine.
Ben Musgrave was the next to go after an ill-advised pull shot, and when Kyle Blanchard was stumped for 20 the score was 101/5 after 31 overs.
Two quick wickets, top-scorer Cam Neal for 41 and captain Jason Trembath for nine, put the brakes on again, with only the application of Thomas and Atkinson keeping the Bay in the contest.
As was the case in the corresponding fixture last year the game went right down to the wire, but in fairness, aside from 20 minutes of mayhem, the Hamilton side had much the better of the majority of the day's play.
Bay of Plenty Development 190/7 (Cam Neal 41, Campbell Thomas 40, Kyle Blanchard 20; Hayden Cargo 3/30) lost to Hamilton second XI (Nick Trebilcock 54, Jake Bezzant 39; Campbell Thomas 4/22) 192/7.