Messi and perennial rival Cristiano Ronaldo have been widely regarded as the best two players in world football for almost a decade now, sharing the last nine Ballon d'Or titles between them while they are once again the top two favourites for this year's award.
Arsenal boss Arsene Wenger went as far as referring to Mbappe as "the new Pele", but Guardiola believes that the "outstanding" Paris Saint-Germain youngster has a lot to prove before he can be compared to the all-time greats.
"Nobody can sit at the same table as Messi. Maybe Mbappe, he's a top player, he will be an outstanding player, I'm pretty sure of that. But to equal what Messi has done in 10 or 12 years, or Cristiano [Ronaldo], for example, we have to wait," he told reporters.
"I appreciate Mbappe wouldn't like me to put more pressure on his shoulders. I think Messi has the numbers of 60-70 games every season, in the big games, always being there to score and assist, never injured, always plays every three days, never injured because he controls his body.
"That's why I don't think we help with hypothetical suitors for him, saying you are going to be the new guy. So let Mbappe have the fantastic career he will have and after we'll see in the future."
Mbappe scored 26 goals in 44 appearances during a remarkable breakthrough season for Monaco last term, earning a mega-money move to PSG where he has already netted twice in as many games.