Messi, 24, set up Barcelona’s opener in their 5-3 La Liga triumph at Camp Nou on Tuesday night before extending the home side’s lead in the 17th minute to equal César Rodríguez’s tally.
The three-time Ballon d’Or winner then netted a delightful second-half brace – the first a delicate lob, the second a composed finish – to ensure he surpassed the milestone that had stood for 57 years.
“We are witnessing the best [player] in every sense,” said Guardiola. “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 doesn’t score goals, he scores incredible goals. He has entered into the history of the club. I want to thank the entire team for the great game and Messi for his achievement.”
The Barcelona coach added: “Leo has rightfully entered into history, there are few players that dominate in this fashion, and he does it.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news