Stefan Savic’s handball conceded the spot-kick and he was sent off, after receiving a second yellow card.
It was a disappointing end for Falcao, who had been presented with a plaque before kick-off and warmly cheered by the home fans when introduced as a substitute in the second half.
To return here for the final on June 1, Atletico will have to beat far stronger opponents than this but, after a slow start, their season appears to be taking shape. They have now lost only once, albeit a thumping by Borussia Dortmund, in 16 matches.
Koke was given too much time to line up his shot from 25 yards but the deflection off 17-year-old Benoit Badiashile was cruel and left goalkeeper Diego Benaglio stranded.
It could have been worse as Thomas Lemar’s curling free-kick grazed the outside of the post but as Atletico’s dominance became entrenched their intensity slackened too.
Griezmann doubled the lead in the 24th minute, receiving on the half-turn and slipping Angel Correa free down the left. Correa’s twisting run put Jemerson on the ground, and he returned to Griezmann to touch into the far corner.