And Messi duly stepped up to score the victor from the spot to put his side above Sevilla and within one point of leaders Real Madrid, although Barca have played two games more.
Performances this season have added to the speculation over his future, with a section of supporters making their unhappiness at the team's progress known during Sunday's narrow 2-1 win over lowly Leganes.
Barca are second in the standings on 48 points and have played two games less than Real but Luis Enrique is still optimistic about their title chances.
However, Barcelona's 4-0 defeat to Paris Saint Germain has led to speculation that Enrique will leave the position in the summer, which will only be increased if they're eventually knocked out of the competition by the French team.
Speaking before that victory, Bartomeu offered some support to Luis Enrique, whose team are second in the league.
'We need to recover our game, ' he said.
"They had good spirit but the players did absolutely everything and when that happens I have no complaints".
Enrique has received fierce criticsm over the past few days with even midfielders Sergio Busquets and Andres Iniesta questioning his tactics.
Yet his side got off to a flying start when Neymar fed Luis Suarez with a through ball into the area and Messi calmly knocked in the Uruguayan's cross.
But it does keep Barcelona within a point of Real Madrid, although Los Blancos have two games in hand. "It's going to be very hard but it's a attractive challenge", said Suarez.
Much-criticised midfielder Andre Gomes received the brunt of the boos as he was replaced 10 minutes from the end.
Messi opened scoring early in the game and after the visitors equalized, he netted the winning goal from the penalty spot in the 90th minute.
Manu Garcia's penalty gave Alaves a valuable 1-0 win away to Deportivo la Coruna, who have yet to win in 2017 and are now squarely in the battle to avoid relegation.