In a dry and breezy but uninterrupted Supersport session, the Fermanagh man knocked Michael Dunlop off the top spot in the dying moments on his final lap, clocking a speed of 114.132mph.
Ballymoney man Dunlop was 1.2s in arrears on his MD Racing Yamaha (113.642mph), with Dean Harrison slotting into third on the DAO Racing Kawasaki, two seconds down on Johnston.
Adam McLean completed the top six on his McAdoo Racing Kawasaki ahead of Jeremy McWilliams, who made a solid start first time out on the Burrows Engineering/RK Racing Yamaha as he replaces the injured Mike Browne in the class.
1 L Johnston (Yamaha) 114.132mph
2 M Dunlop (Yamaha) 113.642mph +1.220s
3 D Harrison (Kawasaki) 113.330mph +2.003s
4 D Todd (Honda) 113.088mph +2.612s
5 A Seeley (Yamaha) 112.923mph +3.031s
6 A McLean (Kawasaki) 112.898mph +3.094s