Messi, 24, struck his latest treble in Tuesday's 5-3 La Liga win over with Granada at the Nou Camp.
Messi equalled the mark of 232 official goals set by Cesar Rodriguez during the 1940s and 1950s when he slotted home Isaac Cuenca's cross in the 17th minute, and then secured the record outright in the 68th minute when he lobbed the ball over Granada goalkeeper Julio Cesar.
The hat-trick came in the 86th minute as Messi went past Cesar and slammed the ball into the roof of the net.
"We are witnessing the best [player] in every sense," Barcelona manager Guardiola said at his post-match press conference.
"He does everything, and he does it every three days. I'm sorry for those that want to sit on his throne, but this lad is the best.
"Hopefully we can enjoy his football for many more years."
Guardiola added: "The day that Leo Messi overcame Cesar, we've had a game from that era.
"Leo has entered history. Those who knew Cesar have told me that he was exceptional.
"I want to thank the team for overcoming all adversity and this guy who is continuing to make history.
"It's all been said before about Messi. He doesn't only score goals, he scores great goals; each one is better than the last. We are seeing the very best in action.
Messi, a three-time FIFA World Player of the Year, has scored 54 goals in 45 games for the Catalan giants in all competitions this season.
Guardiola's remarks, reported on Barcelona's official website, may cause a slight stir in Madrid where Real's former Manchester United forward Cristiano Ronaldo is similarly regarded and nearly as prolific.
But Guardiola is convinced he has the greatest player of the era in his team, and he even agreed that Messi was as significant a figure in football as Michael Jordan was in basketball during the 1990s.
American Jordan ruled the NBA and set a host of records at the peak of his career with the Chicago Bulls, becoming a celebrated sports figure worldwide, even where basketball was a minority sport.
Guardiola said: "You have few players who dominate like this, but he does it. You can compare him perfectly to Jordan."
Team-mates added to the praise for Messi, with defender Gerard Pique saying on fcbarcelona.com: "It's a pleasure to be in the same generation as him, I believe he's the best player in the history of the sport.
"It doesn't matter where he plays, if it's cold or hot, he always proves that he's the best."
Goalkeeper Víctor Valdes added: "Messi will mark an era. He'll be the best ever."