Pakistan looked on course to win after posting a healthy 284 in their innings in the second One day International in Dubai, but the Sri Lankan tail-enders saw their team home with just two balls to spare.
And on Saturday the International Cricket Council (ICC) said Misbah-ul-Haq's team were one over short during the time allotted for the 50 overs.
"Match referee David Boon of Australia imposed the fines after Pakistan was ruled to be one over short of its target, after time allowances were taken into consideration," the ICC said in a statement.
The penalty was accepted by Pakistan without contest so there was no need for a hearing, the ICC said.
Sri Lanka's win on Friday levelled the five-match series at 1-1 after Pakistan had won the first match in Sharjah by 11 runs.
The third match will be played back in Sharjah on Sunday followed by the last two in Abu Dhabi on Wednesday and Friday.
