Younis Khan scored 70 and Dawlat Zadran took two wickets. Pakistan overhauled the victory target in 37.1 overs for the loss of 3 wickets.
Earlier Afghanistan set Pakistan a target of 196 to clinch the one day international.
Karim Sadiq top-scored for Afghanistan with 40 as they were bowled out for 195 after winning the toss. Shahid Khan Afridi with 5-36 was Pakistan's most impressive bowler.