Banyana dominated early proceedings and were rewarded with a goal just before the half-hour mark, thanks to a strike from one of the side's key players Leandra Smeda.
Banyana took a one-goal lead into the break, but knew that they had to score more to avoid dropping points in their first Group C match.
They got two goals in the second period, first through Chantelle Esau before substitute Thembi Kgatlane sealed all three points for the South Africans.
Coach Desiree Ellis will be happy that they converted their chances, but more importantly they kept a clean sheet as this will give them confidence going forward.
Banyana, who started the game against Lesotho with experienced players such as Noko Matlou and Mpumi Nyandeni on the bench, will take on Namibia at Barbourfields Stadium on Friday at 14h00. They then meet Botswana in their final group match on Sunday at the same venue.