South Africa, who had gained a huge 303-run first innings lead, reached 245-8 in their second innings before declaring at tea on the final day.
Set an improbable target of 549, Sri Lanka 'A' reached 89-1 by close.
South Africa decided not to declare earlier as coach Arthur did not want to push his bowlers too hard.
"We didn't want to spend more than 30-40 overs on the field. Scoring wasn't as easy as in the first innings and all we wanted was to give just seven-over spells for our bowlers to get their rhythm," said Arthur.
"There was no point in going flat-out with the Test just two days away," he added.
South Africa shuffled their batting order, sending A.B. de Villiers, Mark Boucher, Ashwell Prince and Nicky Boje ahead of Hashim Amla and Jacques Rudolph, who had made hundreds in the first innings.
De Villiers top-scored with 75 while Rudolph got 58, adding 78 for the eighth wicket with Andre Nel (20 not out).
Leg-spinner Upul Chandana bagged 3-80.
Brief scores: South Africa: 465-4 decl and 245-8 decl (A.B. de Villiers 75, J. Rudolph 58, U. Chandana 3-80); Sri Lanka 'A': 162 and 89-1 (A. Gunawardene 37, M. Van Dort 29).