The Argentine sustained an adductor injury on Tuesday and the opposition coach felt the Blaugrana were significantly hampered by his exit.
Barcelona were not as 'superior' to Villarreal after Lionel Messi went off, according to Yellow Submarine coach Javi Calleja.
"[Messi] played the first half. The team worked to ensure he was not decisive. When he's on the pitch he makes a difference, although it's true he had some discomfort," Calleja said.
"Without Messi they are not as superior, that is evident, but we know how to stop them. We were unable to do more damage or defend better at the beginning.
"We are hurt by the defeat, but happy with our job."
Ansu Fati replaced Luis Suarez with 12 minutes remaining and went close to sealing the three points before seeing an appeal for a penalty turned down following a VAR review.
"I was amazed. He did everything right," Calleja said of the 16-year-old attacker.
"He has huge quality and he is not weighed down by the responsibility. For a football lover he is a joy to watch."
Fati has the ideal role model in Messi, who won The Best FIFA Men's player for the first time at a ceremony in Milan on Monday.
The 32-year-old had finished second to Cristiano Ronaldo twice in the award since it began in 2016 and didn't figure it the top three for the 2018 edition.
"It has been a long time without winning an individual prize," Messi told reporters after clinching the honour.
"It is an award that I have for the first time and it is good to have it."