The England international was replaced just five minutes into the 3-1 win over Reading after being caught by Royals striker Adam Le Fondre.
Moyes said: "I genuinely haven't seen it again but I thought on the pitch it didn't look good.
"Jagielka knew about it and it is a bad one. He will have surgery tonight to stitch up his ankle. It is a bad one because he is a key player for us."
Moyes said he did not know how long Jagielka would be out but the 30-year-old must now be doubtful for next week's FA Cup quarter-final against Wigan.
The incident also reminded Moyes of some of the treatment goalkeeper Tim Howard received in the two previous cup matches against Oldham.
"I'm not happy with the challenges on the goalkeeper in the last two games that have put him out and I am not happy with the challenge today that puts Phil Jagielka out," he said.
"I'm not one who minds challenges. I like a bit of that, if that's what it is. I don't mind robust challenges but not one that puts out arguably one of my best players."