Jayawardene scored 113 as the visitors were dismissed for 461 in reply to Zimbabwe A's first innings of 294. The home side were 28 for one in their second innings at the close of play, a deficit of 139 runs.
The other major contributors to the Sri Lankan total were Thilan Samaraweera, who scored 97, Kumar Sangakkara, with 95, and Thilina Kandamby, who made 52.
Sri Lanka resumed on 66 for two, and Samaraweera and Sangakkara put on 141 for the third wicket with Sangakkara the more aggressive.
Sangakkara faced 93 balls and hit 16 fours and two sixes before being caught behind by wicketkeeper Alester Maregwede off fast bowler Sean Ervine.
Samaraweera and Jayawardene then added 138 for the fourth wicket before Jayawardene and Kandamby shared 63 for the fifth wicket.
Jayawardene was trapped in front by off-spinner Trevor Gripper after 153 minutes at the crease in which he faced 106 balls and hit 17 fours and two sixes.
Gripper, who took three for 22 from four overs, caught and bowled Kandamby to end an attacking innings by the left-hander which featured 10 fours and two sixes and lasted 41 balls.
The home side includes four of the 15 rebels who last month refused to play in a dispute with the Zimbabwe Cricket Union (ZCU) -- former captain Heath Streak, Ray Price, Gripper and Ervine.
