Offspinner Dilruwan Perera took six for 87 for Sri Lanka A.
The hosts rattled up 135 for three from only 19 overs late in the day, with opener Kusal Perera hitting a rapid, unbeaten 62.
Scores: Sri Lanka A 252 and 135-3 (K. Perera 62 not out; D. Bracewell 2-50) v New Zealand A 299-9 declared (C. Cachopa 104, L. Ronchi 47, D. Mitchell 41, A. Devcich 32, Bracewell 25; D. Perera 6-87, C. de Silva 3-60)