Messi, 24, struck his latest treble in Tuesday night's 5-3 Liga win over with Granada at Camp Nou. Messi equalled the 232 goals set by Cesar Rodriguez in the 1940s and 1950s when he slotted home in the 17th minute, before lobbing goalkeeper Julio Cesar to secure the record outright. His third arrived four minutes from time.
"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."
Messi, a three-time FIFA World Player of the Year, has scored 54 goals in 45 games for the Catalan giants 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."