Messi combined to devastating effect with the departing Andres Iniesta - who received a standing ovation on his penultimate home appearance when he was later replaced - to make it three on the stroke of half-time, the forward's 34th LaLiga goal of the campaign.
Subs not used: Ter Stegen, Alba, Gomes, Alcacer.
Villarreal potential starting XI: Asenjo, Rukavina, Ruiz, A. Gonzalez, Gaspar, Cheryshev, Trigueros, Castillejo, Hernandez, Bacca, Raba.
Subs not used: Fdez, Marin, Bonera, Raba. Dembele finished a game where he was man of the match by scoring twice, his first a tap in after a superb individual piece of play by Ivan Rakitic.
Sevilla took full advantage as Wissam Ben Yedder, Miguel Layun and a Sergio Ramos own-goal put them three up, before Real substitute Borja Mayoral and a late Ramos penalty late gave Real a flatteringly close result.
Just as Blaugrana looked to be holding on for the victory, but the Camp Nou was silenced in the second minute of stoppage time.
Coutinho thought he had claimed his second of the night in the 72nd minute when he blasted Dembele's cutback over the line from close range, but the goal was rightly ruled out for an offside against the Brazil international. Seydou Keita's deflected strike gave the hosts a perfect start to the game, but the lead lasted just 10 minutes when Joseba Llorente converted Giuseppe Rossi's cross for the equalizer.
"Considering the heavy number of minutes from the season, the three games remaining may give playing time to some of those who have played less".
It is a common assumption in Spain that the Albiceleste superstar will eventually move into midfield, where he could play an Andres Iniesta or Xavi Hernandez role, and to prolong his career, it might be best for him.
Then came the Messi score. He would like to forget the night quite quickly.
"It is not easy going so many games unbeaten".
Just before that third goal Cillessen had blocked a shot from Costa as Villarreal broke dangerously.
The match gets underway at 7pm UK time. He patiently shook hands with the everyone before disappearing down the tunnel.
When Paco Lopez replaced Juan Ramon Lopez Muniz as coach at the start of March, Levante had won only one of their last 22 games.
It was a wake up call and Ernesto Valverde reacted by bringing on Suarez on the hour.
All joking aside, he represents a threat to the Catalans. Speculation continues over his next destination with the Chinese Super League and Japanese J1 League both possibilities.
FW Luis Suarez, 6 - Worked hard after coming on but didn't have the rub of green in front of goal.