As the old adage says, when you have to go, you have to go.
"(Jose) wasn't happy but there was nothing I could do about it, really. Nature was calling," Dier said after the match. "I heard there was a chance (for Chelsea) when I wasn't on the pitch, but thankfully they didn't score and we've ended up with the win."
Tottenham equalized late - after Dier returned - to send the match to penalties. They were perfect from the spot en route to the 5-4 triumph.
"He had to go, no other chance, he had to go," Mourinho said. "Maybe it's a normal thing when you are completely dehydrated, when you have nothing in your muscles, which was the case. I knew that he had to go, but I was just trying to put some pressure on him to have him back for the remaining time."
Mourinho has been outspoken about his displeasure over a fixture list that has Tottenham playing four matches in eight days.
"Of course, if the football authorities don't care about players, I care, so of course Eric Dier cannot play the match on Thursday," he added.
Spurs meet Maccabi Haifa in a Europa League playoff on Thursday before closing out their busy stretch against Manchester United on Oct. 4.