The muscular Dube smashed an unbeaten 79 off 60 balls that included a half a dozen of sixes and three boundaries which took India's score to 327 for 6 in 47 overs. His whirlwind seventh partnership of 121 off 71 balls with Axar Patel (60 no off 36 balls) gave Indian total an imposing look.
In reply, Chahal warmed up nicely for the upcoming international assignments with figures of 5 for 47 as South Africa were all-out for 258 in 45 overs despite Reeza Hendricks' century.
Hendricks's 110 off 108 balls went in vain as the Proteas weren't exactly comfortable with the slow nature of the tracks.
Wicketkeeper-batsmen Heinrich Klaasen (58, 43 balls, 4 fours, 3 sixes) and Khaya Zondo (30) were the only other batsmen to make notable contributions as Chahal kept the SA 'A' batsmen in check.
Earlier in the day, most of the Indian batsmen got starts but couldn't convert into big scores.
The highly-rated Shubman Gill (46, 47 balls, 7 fours) and captain Manish Pandey (39, 41 balls, 4 fours) were set but failed to score big.
The home team appeared to be heading for a below-par score when Krunal Pandya (14, 25 balls, 1 six) fell to Anrich Nortje, with the score at 206 for 6.
However, Dube and Axar had different ideas. The two southpaws blasted the rival bowlers at will, almost, not sparing the pacemen -- Anrich Nortje (2 for 89 in 10 overs), Beuran Hendricks (2 for 89 in 10 overs) and Junior Dala (1 for 62 in 9 overs).
Dube reached 50 in 46 deliveries, his first in List-A career, blasting some big sixers.
After a quiet start, all-rounder Patel raced to his 50 in just 34 balls as he effortlessly smote a few sixes.
The South Africans didn't get off to a great start, losing opener Janneman Malan (18), who survived after being caught off Deepak Chahar's but it was adjudged no-ball.
Hendricks played positively and was on the lookout for runs. He kept find the boundary but the middle-order failed to offer him support.
Brief scores:
India 'A' 327 for 6 in 47 overs (Shivam Dube 79, Axar Patel 60, Shubman Gill 46, Manish Pandey 39, Ishan Kishan 37, Bjorn Fortuin 2/40, Beuran Hendricks 2/89) beat South Africa 'A' 258 all out in 45 overs (Reeza Hendricks 110, H Klaasen 58, Y Chahal 5/47, Axar Patel 2/39).