Wednesday night's 0-0 draw wasn't the cause of their demise, but an error-strewn 3-0 first leg defeat that left even Messi, Neymar and Luis Suarez too much to do against the team with the best defensive record left in the Champions League.
"A goodbye with pride," ran the headline in both Barcelona sport dailies Mundo Deportivo and Sport.
The hosts were even handed a rousing reception by the near 100 000 fans at the Camp Nou, but there is little time for Barca to lick their wounds as Sunday's El Clasico at La Liga leaders Real Madrid offers a final chance to save their season.
"There was blood, sweat and tears and the Barca fans recognised that with a standing ovation," said Sport.
"The Clasico arrives as a final chance to lift a season undermined by inconsistency."
Even a victory at the home of their eternal rivals might not be enough for Barca to win a third straight league title.
Madrid lead the league by three points and also have a game in hand to come.
However, winning at the Santiago Bernabeu would ramp up the pressure on Zinedine Zidane's men and at the very least offer some joy in a season short on things to shout about.
"We have the chance to put ourselves in the fight for La Liga," said coach Luis Enrique after overseeing his last Champions League game in charge before stepping down at the end of the season.
"I feel happy to be able to work in a club that always wants to win everything. It is not a good night and it is not a good moment for Barca fans, but we will fight until the end."
Without the suspended Neymar on Sunday, Barca will need Messi and Suarez to recover their killer instinct. Of Barca's 17 shots on Wednesday, only one was on target and that came from defender Javier Mascherano.
"Impotent against a wall," said Madrid sports daily AS.
"The shots on target are the ones that count," conceded Enrique.
Emotions ahead of the Clasico couldn't be more contrasting for Spain's two powerhouses.
Whilst Barca have failed to make it beyond the Champions League quarters for two successive seasons for a first time in a decade, Madrid booked their place in a seventh straight semi-final thanks to Cristiano Ronaldo's hat-trick in a thrilling 6-3 aggregate win over Bayern Munich.
Real have always considered themselves the kings of Europe thanks to their 11 European Cups. However, now they seek to end Barca's recent rule of domestic matters in Spain with just a second league title in eight seasons.
Messi and Barca captain Andres Iniesta have been two of the mainstays to Barca's decade of dominance.
A bruised Messi will pick himself up to go again at the Bernabeu in search of his 500th Barcelona goal. And Iniesta insisted the Catalans aren't yet a spent force.
"It is disappointing to be eliminated from the Champions League, but being able to win La Liga depends on winning at the Bernabeu and that is our intention."