Having hit four fifties and a century during the tourists' 3-2 ODI defeat to the Proteas, the opening batsman smashed 78 off 52 balls in Paarl.
Hales blasted nine fours and three sixes, reaching his half-century from just 32 balls, while Eoin Morgan returned to form with 42 off just 13 deliveries as England racked up 202 for six after winning the toss.
Despite Theunis de Bruyn's 56, South Africa A struggled in their chase and were limited to 158 for eight from 20 overs, Reece Topley taking 3-29.
In-form Hales set off like a train, with seven fours in his first 12 balls and 32 of England's first 33 runs, but lost Jason Roy for 22 when he picked out deep mid-on off Andile Phehlukwayo with 57 on the board in the sixth over.
James Vince, fresh from his stint in the Pakistan Super League, contributed 22 off 18 balls before clubbing Wayne Parnell to deep midwicket, ending a stand of 65 with Hales.
Hales holed out off Aaron Phangiso in the 16th over, but Morgan struck five sixes, including three in the 17th from Beuran Hendricks.
The skipper dominated a 49-run partnership in just 17 balls with Jos Buttler, who departed to Phehlukwayo for 29, until he became the second of three victims for Parnell.
Topley, like he did in the final ODI in Cape Town on Sunday, made an early breakthrough by trapping Reeza Hendricks lbw with fourth ball of the chase.
But skipper Morne van Wyk and De Bruyn built a platform for the hosts with a stand of 88 in 62 balls.
The game was up when, with South Africa A requiring 98 from 42 balls, Rashid drew former Yorkshire team-mate David Miller out of his crease and Buttler whipped off the bails.
Willey dismissed Farhaan Berhardien and Parnell late on before Topley returned to the attack for the final over and took the wickets of Phehlukwayo and JT Smuts, for 30, in as many balls.