The visitors were facing humiliation after being reduced to 29-6 in the 13th over and 42-7 after 16 overs before Stubbs (59) and Coetzee (77) got them to a somewhat respectable total of 175.
However, it wasn’t nearly enough, as Sri Lanka A reached their target with seven wickets in hand and 21 overs remaining.
Beyers Swanepoel, Lizaad Williams, Tshepo Moreki each picked up a wicket for SA A.
The visitors won the first match on Sunday by four wickets.
The third and deciding match of the series will take place at the same venue on Thursday.
