Messi opened the scoring with an unstoppable free kick then combined with devastating effect with Luis Suarez to carve Betis open and score a second goal right before halftime.
The Argentine saved his best goal for last, completing a victory which took Barca 10 points clear at the top of La Liga with a spectacular first-timed chip from the edge of the area after playing a one-two with Ivan Rakitic.
Beaten Betis goalkeeper Pau Lopez looked on in awe while the home supporters, renowned for devotion to their side, rose to their feet, bowed down to Messi and chanted his name.
“Even though the opposition concedes goals to Messi they can still enjoy this unbelievable era which he has created, they enjoy it too and today they recognized that,” said Barca coach Ernesto Valverde.
“It’s significant that they gave him this ovation, it’s an acknowledgement. Our rivals’ supporters have to suffer him but they also appreciate him, because of the player he is.
“Leo’s performance was extraordinary, he got three goals but he could have got four, that shows you how good he is.”
Betis coach Quique Setien commended his supporters for their treatment of Messi while saying he felt honoured to work in the same era as the Argentine.
“I really like the fact that our supporters showed their appreciation for a great player, today he really made us suffer,” Setien said.
“It’s only fair and it’s right to recognize this, our fans behaved in an extraordinary way and I’m very proud of them. I’ve seen some magnificent players do great things but no-one can match the things Messi has done over the last 12 years.
“It’s a privilege to have been able to start this era with him and see him in action every weekend.”
The five-times world player of the year moved on to 39 goals in all competitions this season with two months still left in the campaign.
It was Messi’s 51st career hat-trick but he could not recall receiving such applause from a rival team’s fans.
“I cannot remember anything like this before and I’m very grateful for the fans’ reaction,” Messi said. “I’m very grateful to them and happy for the victory, which was very important.”