It was enough to see off fierce rivals Bandon, edging out the West Cork side with a goal in each half.
Insta knocked them out of the Irish Hockey Trophy at the semi-final stage as well as nicking victory in the league in the past month.
This time, the Limerick side got a fortuitous break for their opener as an initial Rosie Pratt shot skewed off to the right of the circle off a defensive stick, allowing Moloney the chance to crash home.
Bandon had made a strong start but were rocked by that concession in the 22nd minute.
And the clincher came in the second half from a clever corner move, the ball going off to the left of the circle rather than the top. It led to an angled pass which Moloney deflected home.
Institute held on for the 2-0 win and now look forward to their Trophy final against Mossley on Saturday in UCD at 12pm.
There was double disappointment for Bandon who lost to Ashton in the U16 Munster final on penalty strokes after normal time had ended 1-1.
Elsewhere, Irish U21 men’s coach Jonny Caren hit out at the lack of funds available to support the development squads in Ireland.
It came in the wake of their series with England in which Ireland won once and lost twice, coming within a missed penalty stroke of sharing the series.
“The important thing for our lads is this is a self-funded programme where there are so few resources given to us,” Caren said.
“That England team has pretty much the same budget as our senior men’s team so we are always going to be behind the eight-ball.
“To me, we have excelled in this series. I hope that people do take note of this, a full-time programme against a, we’ll call it, thrown together group which had three training sessions and then out we go.
“On that, we were supposed to have a training group last week but the EYHL working group put on a fixture [between Pembroke and Lisnagarvey] on what was a designated high-performance day. That’s the measure of support we get.”
Catholic Institute 2 (C Moloney 2) Bandon 0 Under-16 Cup final: Ashton 1 Bandon 1, Ashton win 3-2 on strokes