The England international missed last week's 3-0 win over Southampton with what Guardiola described as a "small problem".
The City boss now says Stones is not fit to play at Wembley in the semi-final but could be back for the Manchester derby next Thursday.
Arsenal training ahead of FA Cup semi-final Thu, April 20, 2017
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Manchester City defender John Stones
He said: "Stones is not fit. Muscular problem.
"He’s out but maybe he comes back for United."
Guardiola added Gabriel Jesus is back in contention after a foot injury to face Arsenal on Sunday.