Skipper Asghar Stanikzai scored highest 57 runs as Afghanistan reached 212-8 in 49.4 overs after bowlers helped the visitors dismiss Bangladesh for a modest 208 runs in 49.2 overs.
Bangladesh won the first match by seven runs on Sunday.
Shakib helps Bangladesh sink Afghanistan in seven-run thriller
The third and final match of the series will be held on October 1.
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