Kompany has spent 11 years at City and enjoyed great success, with the Champions League being the only major trophy he failed to win at the Premier League club.
The 33-year-old Belgian announced a day later that he was to leave and return to Anderlecht, his first club as a professional, and will take up a player-manager position.
City will struggle to replace Kompany's experience and influence, but Guardiola is confident the defender will return one day.
"I think we're going to miss him [Kompany] a lot," Guardiola said during City's trophy parade on Monday.
"I'm going to miss him, but he is going to see us in the future because he is coming back sooner or later.
"It's the best way to say goodbye after an incredible season together. He was a real captain, he helped us a lot.
"Now it's time to have good food, good wine and enjoy this incredible season together. In a few weeks we are going to think about [the future]. Now we are going to enjoy what we have done."
Manchester City have won two consecutive Premier League crowns, finishing ahead of Liverpool this season to claim Kompany's fourth league title.