The hosts declared their second innings closed on 327-3 to set SA A 324 to win on Thursday.
Minod Bhanuka scored 130 and Pasindu Sooriyabandara 113*.
The visitors ended the day on 156-4 after 60 overs, with Zubayr Hamza unbeaten on 24 and Kyle Verreynne on eight.
SA A captain Tony de Zorzi had earlier made 35 before being run out, while Matthew Breetzke (38) and Keegan Petersen (29) also spent significant time at the crease.
Sri Lanka A won the first match in Pallekele by 160 runs after SA A had won the one-day series 2-1.
