Beginning at the overnight score of 36 for one, the visitors lost Warnapura for naught and Mahela Udawatte for 34.
But a 103-run fifth-wicket partnership off 161 balls between T Samaraweera (69) and Chamara Silva (70) saw Sri Lanka A take a vital lead in the match.
While Samaraweera's innings was studded with nine boundaries, Chamara Silva's innings had 10 fours and two sixes.
A late floulrish by Kushal Silva with a crucial 55 studded with 10 boundaries helped them coast past the 300 mark. He and Akalanka Ganegama hit a dogged 52 runs for the seventh wicket to douse any hopes that remained aflame in the hearts of South Zone cricketers.
For South Zone, Kaushik Reddy was the pick of the bowlers with four wickets for 57 runs. Yo Mahesh with three for 74 and S.
Sreeshanth with two for 75 were the other sucessful bowlers.
South Zone began their second innings looking to be in hurry to knock off the deficit. Dinesh Karthik and Robin Uthappa lived dangerously for their respective 16 and seven runs. At stumps South were 24 without any loss.
South Zone 266&24/0 ( Robi Uthappa not out 7, Dinesh Karthik not out 16) Vs Sri Lanka 'A' 327 all out ( Thilan Samaraweera 69, Chamara Silva 70, J K Silva 55, ML Udawatte 34, Jehan Mubarak 32; Kaushik Reddy 4 for 57, Yo Mahesh 3 for 74, Sreesanth 2 for 75)