Palace return to Premier League action six days on from Monday night's 1-1 draw with Champions League-chasing Nottingham Forest.
Wharton was substituted after struggling in the second-half of that match and the Eagles manager confirmed that the midfielder would need longer to recover from his injury.
Providing further details in his pre-match press conference, Glasner said: "No, unfortunately he’s [Wharton] not available.
"If everything goes right he'll be re-integrated in full training next week, and on Wednesday when we start preparing for the [FA Cup] final. He is the only one who can't play. All the others are fit and available."
When asked about Wharton's potential recovery time - ahead of the FA Cup final six days on from the Tottenham game, Glasner was positive about his chances.
“90% he can play [in the FA Cup final]," he added. "But always things can happen. Sunday at Tottenham is too early.
“The pain is too much for this game. His ankle ligament is a little bit damaged, that is the reason, the only reason [he can’t play]."
Match details
- Sunday, 11th May
- 14:15 BST
- Tottenham Hotspur Stadium
- Live audio commentary on Palace TV+