The 22-year-old has not appeared since the Citizens' 3-1 win over Hull City on April 8 due to a muscular problem, seeing him sit out the last six matches.
Guardiola could now turn to Stones for games against West Bromwich Albion and Watford, but midfielder Fabian Delph is crocked once more and is unlikely to feature again this term.
"John has come back. Delph has injured his leg. I don't think he will play in either game," Guardiola told reporters.
Stones has made 38 appearances for Man City in all competitions since joining from Everton in a £47.5m deal last summer.