Aquinas answered back with a powerful effort from close range to captain Reed Wilson to narrow the advantage to a point, but errors saw Bethlehem extend their lead through a converted try to standout blindside flanker Matt Leppard.
The 13-5 advantage represented a good return for Bethlehem before Aquinas fullback Jesse Church changed the match just before the break.
A back foot scrum ball went wide and somehow found Church on the outside of a rushing defence.
The fullback put a fend and a swerve on from 60 metres out and showed a clean pair of heels to bring his side back into it despite a late penalty increasing the deficit to 16-10.
Bethlehem went scoreless in a second half in which Aquinas' larger forward pack mauled at every opportunity.
Openside James Sharp was the beneficiary of an impressive rolling maul that made it 16-15, before Bethlehem indiscipline gifted Aquinas a penalty out in front with only minutes remaining.
Talented hooker Anaru Bidois made no mistake, extending his side's unbeaten streak at home this season.
Reed was proud his players had defended the Te Kani Shield despite gifting Bethlehem a handy advantage.
"They had it all over us in the first half so it was great to take it back to them up front," he said.
"It definitely means a lot to the boys. This is the first year we have got any silverware so we want to keep it for as long as we can."
Aquinas College 18 (Reed Wilson, Jesse Church, James Sharp tries; Anaru Bidois pen) Bethlehem College 15 (Matt Leppard try; Jack Preston 3 pens, con) HT: 10-16
