Setien left Griezmann on the bench for the third time in four games.
The Barca boss opted for four in midfield against Atletico and when he decided to introduce an attacker, he called on Ansu Fati.
Griezmann, a €120million signing from Atletico last summer, finally came on with only three minutes of additional time remaining.
“He’s an important player but I understand it’s tough for him to come on with so little time left.
“I will speak with him [on Wednesday]. I won’t say sorry because [it’s about] decisions, but I understand he may feel bad and I feel bad for him because he’s a great person and a great professional,” Setien told a news conference.
Griezmann, 29, featured regularly in his first season at Camp Nou, scoring 14 goals, but has fallen out of favour in recent weeks.