The South African appeared as a substitute for the fifth time in eight games, having failed to score in two starting roles, first in the 2-2 draw at Sporting Huelva before a 4-2 loss to Deportivo La Coruna.
The 2018 African Women's Footballer of the Year played a significant role in her side's third victory of the campaign as Honoka Yonei set her up to bag the late winner three minutes from time.
Kgatlana's goal was her fourth in eight outings for Eibar as she featured for 31 minutes after replacing Nigeria's Charity Adule. Equatorial Guinea's Ruth Alvarez lasted the final 31 minutes.