The left-hand batter now has eight centuries to go with her 15 half-centuries in ODIs.
Mooney, Laura Wolvaardt, Nat Sciver-Brunt, Meg Lanning, Harmanpreet Kaur and Smriti Mandhana all dropped one spot each as Athapaththu moved up from seventh place in the rankings.
Athapaththu has now emulated another left-handed opener, Sanath Jayasuriya, who is the only Sri Lankan man to top the ODI batting charts.
During her whirlwind knock in the third ODI, Athapaththu put on 190 runs for the third wicket with Nilakshi de Silva, which is the highest partnership for Sri Lanka in women's ODIs. Her heroics helped Sri Lanka win their first bilateral series against New Zealand.