Pakistan had salt rubbed into their wounds when they were fined for their slow over-rate durng a narrow two-wicket defeat against Sri Lanka on Friday.
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.
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.
In accordance with the ICC code of conduct, players are fined 10% of their match fees for every over their side fails to bowl in the allotted time, with the captain fined double that amount.
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.
Both teams will also play three Tests after the one-day series.