The Summit Fin pair were able to temporarily halt the victory march of the Investec-songo-Specialized team of World Champions Annika Langvad and Anna van der Breggen who had convincingly won every other day of racing.
Lill and Morath finished the stage in a time of 5:20:42, just over four minutes ahead of Langvad and Van der Breggen, with Silverback-Fairtree's Jennie Stenerhag and Mariske Strauss finishing third, seven minutes further back - despite a big crash for Strauss when a rider went down in front of her near the finish.
Going into Saturday's and Sunday's final 159km of racing, the Investec-songo-Specialized duo still hold a 21-minute lead over Lill and Morath with Ariane Lüthi and Maja Wloszczowska (Kross-Spur Racing) third, another 30 minutes further back.
Lill and Morath broke away with the race leaders soon after the start and at the first water point the two teams had already established a significant lead over their rivals. Van der Breggen then crashed and punctured which meant the South African and her German partner were able to build a two-minute lead at the halfway point.
With Van der Breggen struggling to get back into a rhythm after her crash and the compulsory portage down the Gantouw Pass, Investec-songo-Specialized opted to ride a steady pace and minimise their losses. Their decision to back off from chasing the stage win allowed Summit Fin to double their lead to the finish.
"It was very hard out there today," said Lill after the finish. "Those little bumps on the route profile never seemed to end. It just felt like non-stop climbing today.
"Anna had a crash in front of me on an early descent and we got a gap and then just kept it steady until the end."
The South African was very pleased to have made it a double win for South Africa, in both the Men's and Women's categories, on the Queen Stage.
"The spectators were amazing out there ... they really got me through today. It is awesome for South Africa with Matthys Beukes and Philip Buys winning too. With Stellenbosch being a cycling hub for South Africa, there were so many spectators out there - I got tears in my eyes with them all shouting for me.
"We did not expect to win the stage. We knew the climbing suited us, but Annika and Anna are a pretty formidable pair, so to pull off this win is pretty special."
Van der Breggen had no obvious reason for her struggles after the Investec-songo-Specialized dominance before Friday.
"The beginning was fine," said the Olympic Road Race Champion as she waited for the podium presentation. "But after my crash I just felt really bad. Then when we fixed the tyre we stood still for a while. All of that and then after the portage, I just felt really bad.
In the race for the African Women's Jersey, Theresa Ralph and Sarah Hill of team Galileo Risk finished the stage as the sixth women overall and maintained their big lead in the competition.
Saturday's penultimate stage starts and finishes in Stellenbosch and sees riders complete an 89km out-and-back course on the trails around the historic town.
2019 Stage 5 Women's Results
1. Summit Fin 54-1 Candice Lill (South Africa) 54-2 Adelheid Morath (Germany) 05:20.42,1
2. Investec-songo-Specialized 50-1 Annika Langvad (Denmark) 50-2 Anna van der Breggen (Netherlands) 05:24.48,0 +4.05,9
3. Silverback - Fairtree 52-1 Jennie Stenerhag (Sweden) 52-2 Mariske Strauss (South Africa) 05:32.12,2 +11.30,1
1. Investec-songo-Specialized 50-1 Annika Langvad (Denmark) 50-2 Anna van der Breggen (Netherlands) 23:09.42,2
2. Summit Fin 54-1 Candice Lill (South Africa) 54-2 Adelheid Morath (Germany) 23:31.04,5 +21.22,3
3. Kross-Spur Racing 53-1 Ariane Lüthi (Switzerland) 53-2 Maja Wloszczowska (Poland) 24:01.10,5 +51.28,3
4. Silverback - Fairtree 52-1 Jennie Stenerhag (Sweden) 52-2 Mariske Strauss (South Africa) 24:09.06,5 +59.24,3
5. Meerendal WIAWIS Rotwild 51-1 Sabine Spitz (Germany) 51-2 Nadine Rieder (Germany) 24:29.07,9 +1:19.25,7
6. Galileo Risk 56-1 Theresa Ralph (South Africa) 56-2 Sarah Hill (South Africa) 25:41.20,0 +2:31.37,8
7. FreakShow SCOTT 57-1 Sonya Looney (United States of America) 57-2 Catherine Williamson (England) 26:22.27,5 +3:12.45,3