Phalula, who finished on the podium at every race in the campaign, won the Johannesburg leg, held in warm conditions, in 35:08.
Zimbabwean Rutendo Nyahora charged to the front in the early stages, but Phalula surged up a long hill to take the lead before the 3km mark, and she never looked back.
Having led the series standings by 14 points going into the race, she comfortably secured the R150 000 first prize.
Nyahora held on to finish second in 35:49 and Phalula’s twin sister, Lebo, took third place in 36:22, just three weeks after making her marathon debut in Cape Town.
Many of the nation’s top road runners were not in contention, either coming off recent marathon races or injuries, with Nolene Conrad finishing seventh, and Rene Kalmer and Mapaseka Makhanya ending 10th and 11th respectively.
Irvette van Zyl, competing in her first race since giving birth to son Louis last month, finished a respectable 12th in 38:20, and husband LJ van Zyl, a 400m hurdles specialist, made a rare appearance on the road by completing the 5km fun run while pushing their son in a pram.