Bangladesh, seeking their maiden series win over the Proteas, will need to score 170 runs in 40 overs according the Duckworth/ Lewis Method.
The match was reduced to 40-over-a-side as rain intervened midway through the South African innings halting the play for nearly three hours at the Zahur Ahmed Chowdhury Stadium.
South Africa, opting to bat first, were in dire straits with 4-78 in 23 overs when the rain came.
JP Duminy topscored 51 off 70 balls and put 63 runs with David Miller (44) for the fifth wicket to help the visitors recover before he became the last man dismissed.
When Shakib forced Amla to edge a catch to wicketkeeper Mushfiqur Rahim, he became the second Bangladeshi to take 200 ODI wickets after another left-arm spinner, Abdur Razzak who took 207 wickets.
It also secured Shakib a place in the elite club of all-rounders who have taken 200 wickets and scored 4,000 runs in ODIs.
Only Sri Lanka's Sanath Jayasuriya, South Africa's Jacques Kallis, Pakistan's Shahid Afridi and Abdul Razzak and New Zealand duo Chris Harris and Chris Cairns achieved the double before Shakib.
Mustafizur and fellow paceman Rubel Hossain also grabbed two wickets each giving away 24 and 29 runs respectively.
The two teams will play a two-Test series after the ODIs with the first Test starting in Chittagong on July 21.
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