Atal (104) and Abdul Malik (84) put on 191 runs for the first wicket and an unbeaten 29 from captain Hashmatullah Shahidi lifted the tourists to 286-6 off 50 overs.
Zimbabwe, who won the toss, were in trouble from the outset when replying with Ben Curran run out off the final ball of the first over.
Only Sikandar Raza (19 not out) and Sean Williams (16) reached double figures and the home team were bundled out for 54 in 17.5 overs at Harare Sports Club.
Afghan bowlers Allah Ghazanfar (3-9), Naveed Zadran (3-13) and Fazalhaq Farooqi (2-15) wreaked havoc.
"I am very happy with my performance and that of the team. We won a fantastic game of cricket," said player-of-the-match Atal.
"Abdul and I coped well. We supported each other and that is why we did well and the team did well. I did become a little nervous as the century drew near."
Shahidi said: "I was very impressed with the way the openers batted. The credit goes to them. We outclassed them in all departments.
"When batting, I found the wicket a bit tricky. I believed we had enough runs to win. We gave 100 percent and did well.
"Everyone takes responsibility in this team and everyone knows their role. We want to carry on with performances like this."
Atal, a 23-year-old who made his ODI debut last month, struck four sixes and eight fours in his 128-ball knock before becoming a victim of Newman Nyamhuri (3-53).
Malik also fell to Nyamhuri, making his second ODI appearance, after an innings that included a six and 11 fours.
It was another dark day for Zimbabwe in the 50-over format after the first match against Afghanistan two days ago was called off after just one hour due to rain.
Zimbabwe share with the United States the unwanted record of the lowest ODI international score having made just 35 against Sri Lanka in Harare in 2004.
Their 38, against Sri Lanka in Colombo, and 44 against Bangladesh in Chattogram are among the seven lowest ODI scores.
Brief scores
Afghanistan 286-6 in 50 overs (Sediqullah Atal 104, Abdul Malik 84, Hashmatullah Shahidi 29 not out; Newman Nyamhuri 3-53, Trevor Gwandu 2-70) v Zimbabwe 54 in 17.5 overs (Sikandar Raza 19 not out, Sean Williams 16; Allah Ghazanfar 3-9, Naveed Zadran 3-13, Fazalhaq Farooqi 2-15)
Result: Afghanistan win by 232 runs
Series: Afghanistan lead 1-0 with one match to play on Saturday
Toss: Zimbabwe
