Phalula, who had opened a gap of more than 200m at the 8km mark, won the race in 34:34, with Zimbabwean Rutendo Nyahora producing a late surge to finish second just six seconds off the pace.
Mamorallo Tjoka of Lesotho, who will aim for her ninth Soweto Marathon title next month, took third place in a tight contest for the podium positions, crossing the line in 34:43.
Phalula’s twin sister, Diana-Lebo, who finished fifth, did enough to secure the overall series title and a new Nissan Micra.
“I’m very happy for my sister, but next year I want to win the series myself,” said Lebogang.
The siblings won four of the five races between them in this year’s Grand Prix series.
Results: 1 Lebogang Phalula 34:34, 2 Rutendo Nyahora 34:40, 3 Mamorallo Tjoka 34:43, 4 Irvette van Zyl 34:58, 5 Lebo Phalula 35:21, 6 Rene Kalmer 36:02, 7 Mapaseka Makhanya 36:27, 8 Tebogo Masehla 36:44, 9 Isabella Jepchumba 37:10, 10 Christine Kalmer 37:21