The tourists scored a challenging 8-302 in Kandy on Tuesday with Craig Ervine making a 98-ball 91, Sikander Raza hitting 56 in 46 balls, and Sean Williams and Regis Chakabva scoring 48 and 47 respectively.
Sri Lanka used eight bowlers in an attempt to slow the flow of runs with Jeffrey Vandersay (3-51 off nine) the pick.
The home team made a poor start, being 3-31 in the eighth over and 4-63 in the 15th.
But Shanaka, coming in at No.6, revived the innings adding 118 in 20 overs with Kamindu Mendis (57) and 66 in ten overs with Chamika Karunaratne (34).
When Shanaka brought up his hundred with a six the chase looked promising, but he was out next ball leaving Sri Lanka 56 to win in 32 balls.
They fell short, losing by 22 runs with Tendai Chatara taking 3-52 and Blessing Muzarabani 3-56.
"We were under a bit of pressure to win today," said Ervine. "Hats off to the boys for coming out and showing that desperation to pull off the win. The seamers did really well to get those early wickets for us."
"We didn't bowl well at the start and then our top order also didn't click," siad Shanaka. "Hopefully both will fire in the next game. We need to have better plans."
The third and final match is in Kandy on Friday.
