Vydra saw second-half action for defeat at home to Southampton.
Clarke told the club's official website: "I didn't include Diego in the squad at all on Saturday after he travelled with Uruguay and went to Japan.
"When he came in to the club he was a little bit behind us in his preparation.
"Vydra - I have to be honest - I haven't seen much of. He came in for his medical last week and then went away with the Czech Republic.
"I thought he looked quite lively when he came on and I know he's done a full pre-season with Udinese so I think Matej will pick up the pace quickly."
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