The incident took place in the fifth and final one-day international at the R. Premadasa Stadium in Colombo, which Sri Lanka won by two wickets. The hosts also won the series.
“As this was Pakistan's first serious over-rate offence in the past 12 months, Chris Broad of the Emirates Elite Panel of ICC Match Referees handed Misbah two suspension points while each of his players received a 40 percent fine (10 percent for each of the first two overs and 20 percent for the additional over),” ICC said.
Misbah pleaded guilty to the charge and the subsequent penalties were accepted without the need for a formal hearing, the governing body said.In March, Pakistan was also fined for a slow over-rate in the opening ODI of the Asia Cup against Bangladesh in Dhaka.
However, on that occasion, Pakistan was slow by only two overs and the matter was treated as a minor over rate offence.
The second Test begins at the Sinhalese Sports Club grounds on June 30. The visitors then take on the hosts for the third Test at the Pallekele Stadium in Kandy from July 8.
Pakistan earlier drew the Twenty20 series with Sri Lanka.