The 31-year-old skipper has not featured in the Premier League since the 2-1 win at Bournemouth on August 26.
Despite training again on Friday, Kompany is unlikely to be available against the Hornets, although he could be recalled for Wednesday's Carabao Cup match at West Brom.
"Vinny played today," Guardiola said on Friday afternoon. "He came back and trained with us. I think for the next days, he will be able to play again."