Star striker Kris Boyd was on target for Killie but could not deny the Dons a 2-1 triumph at Pittodrie which Johnston felt was a disappointing performance.
"It was disappointing. We know we have to improve. We gave Aberdeen too much space, and they countered on us a few times and created a lot of chances," he said.
"The positive was the second half performance to come back into the game.
"We got a goal back and were unlucky not to score another one, but we know we have to defend better as a team.
"The goal shows you the quality Kris has. He's not quite match fit yet but when he is, he'll be a handful for any defender."