The Gers chief banished the veteran 37-year-old from his first-team squad following a meeting to discuss the 2-0 loss to Celtic.
Miller subsequently played and scored in a 3-3 behind-closed-doors friendly against Morton last Saturday during the international break.
And, after the pair sat down for clear-the-air talks this week, Caixinha revealed that they have now put their differences to one side.
"[He reacted] with full respect," Caixinha said about Miller's exclusion from the squad.
"He's a senior player and he understands these things. We spoke and we clarified everything regarding those decisions.
"Sometimes it's important to justify your decisions. Other times, I don't have to justify anything. But we clarified everything."