The away side were camped in Mary's territory for most of the second half, initiating wave after wave of attacks.
The slightly understrength Mary's side did well to prevent a try in the third quarter but the Bruff pressure intensified and they managed to force a penalty try on the hour mark as well as two impressive tries from full-back Patrick Thompson.
Asked if he was pleased with his side's performance in the 46-27 win, Mary's player-coach Shaun McCarthy said: "No, not particularly. Bruff were all over us in the second half.
"We were looking to rotate the squad. But physically Bruff dominated us in the second half which is a bit disappointing at home, but we will move on."
With a fantastic record at home and away this season, Mary's could be forgiven for going into this game full of confidence, however McCarthy was slightly critical of the number of points conceded in the second half.
"That's about as many points as we have conceded in AIB League Division 1A this year, it is a bit of a setback.
"But we did make a lot of changes this week. A lot of guys were getting their chance today but there are no excuses," he admitted.
"We're very happy with the progress we've made this season and that's why we did give different players a run today.
"It is a long season, we know we're going to get injuries down the line and we still are competing in three competitions, therefore we need that strength in depth.
"So it is a positive score, we still put 46 points on the board so we'll take that out of it," added McCarthy.
Overall, Mary's showed that they could step up their game when needed. This was evident when they responded to the Bruff penalty try with a ruthless phase of dominance by scoring two tries within eight minutes.
Bruff assistant coach Peter Malone granted that it was a case of too little, too late for his side.
"Definitely too little, too late as regards today's result. But we're a young team, we've got a lot of injuries at the moment so definitely at half-time we were looking at serious trouble but credit to the lads, they came back very well in the second half," he said.
"Mary's are an excellent team, joint top of Division 1A and we're in the middle of Division 2, but I think overall it was a fair performance and a fair reflection of where both teams are."
Bruff were subjected to a 54-13 hammering by Lansdowne in Division 2 last weekënd. Asked if this cup encounter at Templeville Road was a step-up, Malone replied: "Funny enough, I didn't because Lansdowne had a super team out that day.
"Lansdowne are really very strong in Division 2 so it probably wasn't that much of a step-up.
"There's a bit of a difference between a club like us and Mary's at the moment, but that's something we'll work on over the next few months."
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