Leg-spinner Lasith Malinga dropped a sitter at long-on when Hafeez was on 26 in the 18th over Sunday. The Pakistani vice-captain went on to hit a career best 140 not out in his team's imposing total of 326-5 in 50 overs.
Sri Lanka were bowled out for 213 in 44.4 overs, losing by 113 runs and conceding a 2-1 lead. Pakistan won the first match by 11 runs while Sri Lanka took the second by two wickets.
Mathews said the dropped catch was crucial.
"It was pretty crucial and Hafeez went on to get a big one. We let him go and he got them a big score and it was unfortunate we let him go," said Mathews.
Mathews said his team's otherwise good fielding was not up to the mark on Sunday.
"We can't blame it on one man, to be honest. I thought our fielding was also a let down and also chasing a total like 320 plus we needed a good start but we kept losing wickets at regular intervals and we could not really get on from there."
Mathews said Umar Gul's return from injury was a boost for Pakistan.
"We all know that Gul is a very good bowler," said Mathews of the paceman who took two early wickets in his first spell of five overs, before finishing with 3-19.
"He had been hit by injury we know what kind of a bowler Gul is and we had to be a bit cautious but unfortunately we lost a couple of wickets to him and he got us in the back foot early on," said Mathews of Gul who was playing his first match since March after a knee operation.
Pakistan captain Misbah-ul Haq also hailed Gul's return.
"We were missing his experience in the death (final) overs and his return has certainly boosted our bowling," said Misbah, who chipped in with a 26-ball 40 in Pakistan's innings.
"We have to be at our best in the next two games to take the series," said Misbah of the last two games in Abu Dhabi on Wednesday and Friday.
The two teams will also play three Tests after the one-days.