The decisive goal came from Nobahle Mdelwa, who converted a penalty with a firm shot over Lesotho goalkeeper Mamakhabane Makibinyane.
The result was a positive step for Banyana coach Desiree Ellis as she continues to expand her squad ahead of the Women's Africa Cup of Nations (Wafcon), set to take place in Morocco this July.
The friendly was part of a series of matches designed to widen the player pool, allowing new talents to gain experience at the international level.
Both teams are expected to make changes when they meet again on Tuesday, with the coaches keen to provide more players with an opportunity to prove themselves.
Despite the narrow margin, the match served as a valuable exercise for Banyana Banyana, who are looking to fine-tune their squad ahead of the prestigious continental tournament.
"We have had a challenge putting a team together previously," Ellis said ahead of the match.
"So we want to make the core group bigger and we want to see who we can add to the current core group, so it's players that played at the Cosafa, and those that have also stood up in the past season.
"There are also some of the players that have done well on the U-17 and U-19 teams.
"We want to have a look and see if they can step up and if we can add them to the core group because this might be the only opportunity we can get because the next FIFA date is in two matches and then it will be preparation for Wafcon."
South Africa head coach Desiree Ellis has officially named her final 23-player Banyana Banyana squad for the 2025 CAF Women's Africa Cup of Nations (WAFCON) in Morocco, as the reigning champions look to defend the title they famously lifted in 2022.
Banyana Banyana completed a dominant Cosafa Tri-Nations Series campaign with a 2-0 victory over Zambia on Tuesday, wrapping up their WAFCON preparations with an unblemished record.
Banyana Banyana head coach Desiree Ellis has named her 30-woman squad to take on neighbours Lesotho in two international friendly matches later this month.
Banyana Banyana suffered their third consecutive international friendly defeat, falling 3-0 to Jamaica at the Catherine Hall Sports Complex in Montego Bay on Saturday morning.
