Saul jinked past a clutch of Bayern defenders before curling into the corner, giving the home side a narrow first-leg lead to take to Germany.
Bayern dominated the second half, David Alaba hitting the bar from 35 yards and Arturo Vidal’s strike forcing a save.
Fernando Torres poked against the post in a rare counter as Atletico held on.
The teams will meet at Bayern’s Allianz Arena on Tuesday to decide who will meet Manchester City or Real Madrid in the final on 28 May.
Man of the match – Saul