However, the impressive Jonny Hepworth sent Niall O'Brien through for a try deep in injury time to send the travelling supporters home happy.
St Mary's young side started the game well, with veteran John McWeeney and Willie Duggan prominent early on. Six minutes in, out-half John Sexton threaded a clever kick through the Clontarf cover and James Norton won the race for the touchdown.
Clontarf rallied well; within five minutes Peter O'Brien made in-roads up the right before full-back Darragh O'Shea finished the move with a try, and then he added a penalty to his successful conversion. Sexton levelled matters with a penalty before Clontarf's quick thinking at a line-out flummoxed their opponents: Ben Gissing thundered upfield and wing Derek Keane got the try.
It looked even worse for Mary's when second row Fergal Logan was sin-binned near half-time, but a loose Clontarf pass was intercepted by McWeeney, who galloped 80 yards to touch down under the posts. Sexton's conversion made it all square at the break, 17-17.
The home side took the fight to Clontarf after the break, and Sexton landed a difficult penalty to edge them ahead.
But Clontarf kicked three penalties in a row to the corner as a signal of intent, and eventually Keane crashed through two tackles for a try.
Another O'Shea penalty gave Clontarf breathing space and in the 82nd minute O'Brien clinched them the bonus point.
: R Smyth, J Norton, P Lynn, R Gannon, J McWeeney (c), J Sexton, J Kilbride, M Duggan, O McCormack, C O'Byrne, E Keane, G Logan, W Duggan, C Potts, H Gervais.
: M Aboud for Keane, 30; F Lynch and B Moran for Gannon and O McCormack, 55; B McCormack for Duggan, 65; S Gibney for Kilbride, 67.
: D O'Shea, N O'Brien, M Hewitt, B O'Donnell, D Keane, P O'Brien, D Geraghty, J Wickham (c), N Carson, R Sweeney, B Gissing, A Wood, J Ellison, P Perdue, D O'Brien.
: J Hepworth for O'Donnell ht; F O'Loughlin and D Quinn for Geraghty and Perdue, 55; A O'Donnell for Sweeney, 60.
: D Courtney (IRFU).