While there were moments of brilliance from the South Africans, they were guilty of making too many mistakes, which allowed their opponents to remain in the fight in the first half.
If the Bok Women have ambitions to entrench themselves as a global top-10 team, they will have to start playing like one and can't afford the number of unforced errors and soft moments they had in the first half against Uganda.
It looked like they struggled with the referee's interpretation and lost too much possession at the breakdowns, while they also conceded too many penalties.
The Ugandans took a 12-0 lead in as many minutes with two tries as the South Africans looked asleep in the early exchanges, and although they wrestled back control of the match, it took the Bok Women 37 minutes to finally take the lead.
Shaunique Alexander scored on debut when she finished after the Bok Women managed to hold onto the ball in their opponents' half, crossing in the left-hand corner following a strong run by Thandile Mazwi (pictured below) in the 17th minute.
Her fellow wing, Alichia Arries, scored in the 30th minute and with Jakkie Cilliers adding the extras, it was 12-12.
Promising No 8 Logan Welman put the Bok Women in the lead when she crashed over for a converted try after another strong run and offload by Mazwi to hand South Africa a 19-12 lead in the 37th minute.
Debutant lock Zethu Gcaza was sent to the sin bin for a high tackle shortly before the end of the first half and Uganda made it count with their third try to make it 19-17 at the break.
The Bok Women improved in the second half as they kept Uganda scoreless until a last-minute penalty goal, while their bench make an impact, but it was still not the commanding performance they would have hoped for.
Two converted tries in the first 12 minutes of the second half, by Thamie Yeko from a quick-tap penalty, and a first Test try for Naima Hlatshwayo, put some daylight between the Bok Women and Uganda, but the East Africans refused to lie down. It took another 16 minutes for the South Africans to score again when Faith Tshauke went over from a good lineout drive.
Arries grabbed her second try when the ball was sent wide from a lineout steal, and Cilliers' conversion - her sixth from seven attempts - sealed the deal in what was a scrappy win for the Bok Women.
Scorers:
Springbok Women 47 (19) - Tries: Shaunique Alexander, Alicia Arries (2), Logan Welman, Thamie Yeko, Naima Hlatshwayo, Faith Tshauke. Conversions: Jakkie Cilliers (6).
Uganda 20 (17) - Tries: Peace Lekuru, Gertrude Kateesa, Mastula Nambozo. Conversion: Bushira Namutebi. Penalty goal: Namutebi.