Shrubsole took 4-29 in Benoni, including three wickets in 10 balls, as the hosts stumbled from 119-1 to 196 all out, despite Trisha Chetty’s defiant 90 from 122 deliveries.
England’s chase was punctuated by two rain delays, but Sarah Taylor (41no) top scored on the day of her 99th ODI cap as the tourists reached their new target of 150 from 28.3 overs, well within the revised 35-over limit, in Mark Robinson’s first game as head coach.
Shrubsole and Katherine Brunt kept South Africa’s openers under control early on after the visitors lost the toss, with Shrubsole rewarded at the end of the eighth over when she trapped Laura Wolfvaardt (5 from 24) lbw with the score on 26.
Chetty’s steady stand of 93 from 135 balls with skipper Mignon du Preez (38) put the home side in a healthy position at the 30-over mark, but Shrubsole struck from consecutive balls in the 31st, having Du Preez caught at midwicket by Heather Knight and then rapping Marizanne Kapp on the pads for a first-ball duck.
Shrubsole bowled Lizelle Lee (12) in her next over as South Africa went on to lose nine wickets for 77 runs, Jenny Gunn (2-25) and Knight (2-42) sharing four scalps.
Amy Jones (34) then clubbed six fours prior to holing out to deep midwicket as England reached 63-2 from 13.1 overs before the first rain break, Lauren Winfield (10) the other player to depart after being caught at first slip.
Charlotte Edwards (33) chopped on upon the restart having put on 43 with long-time colleague Taylor, while the second interruption came after the latter and Knight (26no) had swelled England’s score to 120-3 from 25 overs.
Taylor and Knight’s task when play resumed was to collect 30 runs from a maximum of 60 balls, a challenge the pair completed with ease, posting their half-century stand when Taylor biffed the match-winning boundary.