Having picked up 12 wickets in the first match of the series, Muthusamy claimed figures of 5-101 in 26 overs as the hosts scored 257-7 in 66 overs on a rain-affected day.
Pasindu Sooriyabandara top-scored for Sri Lanka A with 41, with Ramesh Mendis unbeaten on 38.
Pace bowlers Lutho Simpala and Lizaad Williams took the other two wickets to fall.
Sri Lanka A won the first match in Pallekele by 160 runs.