Messi converted from the spot 10 minutes before half-time and then the Argentine’s cross forced Pau Torres into an own-goal after an early double from the 17-year-old Ansu Fati had already put Barca in charge.
It meant Barcelona’s past, present and future were all among the goals on the same afternoon as Luis Suarez, whose departure was confirmed on Thursday, marked his Atletico Madrid debut by scoring twice in a 6-1 win over Granada.
In a farewell message to his best friend and former neighbour last week, Messi took another swipe at the Barca board by saying he was not surprised by the clumsy way Suarez’s exit had been handled.
His complaints raised doubts about his state of mind heading into the season and at the end of a traumatic summer in which Barcelona’s greatest ever player admitted he was being forced to stay against his will.
Koeman insisted on Saturday that Messi had been “leading by example” in training and his confidence was repaid at Camp Nou, where the striker, and club-captain, delivered an excellent display.
“It is always important to win games, you gain confidence,” said Koeman. “This result helps us to improve and be clear about what we want.”
Messi’s anger over Suarez shows he is still at odds with Barcelona’s president Josep Maria Bartomeu and his long-term future remains uncertain, but on the pitch, he delivered.
Victories and goals could encourage him to stay, not to mention the talented Fati, who on this evidence can be a huge asset for his captain’s hopes of winning back the title.
“Ansu is a young player who has to seek consistency in his game and in his performances,” said Koeman. “He has shown that he has a great future at Barca and I am very happy with him.”
Fati became Spain’s youngest ever international scorer earlier this month and the teenager, deployed on the left of Barcelona’s attacking trio, made an explosive start to the season for his club.
He fired Jordi Alba’s pull-back into the top corner and then drove a second inside the post after Philippe Coutinho was allowed to carry the ball forward and spread it wide.
Fati then won the penalty, his feet too quick for Mario Gaspar, and Messi slid in his first goal of the season before his cross, aimed for Sergio Busquets, was poked into Villarreal’s net by Pau.
‘One bites, one hits’
Messi might have been watching a few hours earlier as Suarez scored twice and set up another in a sensational 20-minute debut for Atletico.
Suarez laid on a goal two minutes after coming on as a substitute, his sumptuous pass finished off by Marcos Llorente, before scoring himself with a powerful header at the back post.
He then added another in injury-time, following up his own shot to make it six for a rampant Atletico at the Wanda Metropolitano.
“Sometimes it is important to have a change as a player,” said Suarez.
“I’ve come to a club that has given me a spectacular welcome, it shows in the atmosphere, you get a good impression from the beginning, and you can see that on the pitch.”
Diego Costa said with a smile: “It’s great. One of us bites, the other one hits.”
Costa had earlier given Atletico the lead but it was the 31-year-old who made way for Suarez, and he raised doubts about his future after the match.
“I leave my future up to the club. I spoke with the club, with the coach, I made it very clear what was happening, that if I am here, I will fight,” said Costa.
“If they see the possibility of me leaving, I’ll accept it. I don’t want to be a burden.”
Angel Correa and Joao Felix scored Atletico’s second and third to put Granada out of sight. The 20-year-old Felix was the best player on the pitch before Suarez stole the show.
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