Approaching Champions League games will go ahead behind closed doors, as UEFA is allowing clubs to open stadiums up to 30 percent of capacity.
The Uruguay striker, who joined Barcelona from Liverpool in 2014, leaves the club having won the Champions League, four La Liga titles and four Copa del Rey trophies.
US midfielder Tyler Adams' 88th-minute winner earned the German side a showdown with Paris St Germain in the quarter finals of the Champions League.
Alvaro Morata scored twice to help Atletico Madrid to a 3-0 win over relegation-haunted Mallorca and stretch their unbeaten La Liga run to 12 games, as the victory consolidated their third place on 62 points to stay well on course.
The result gives Real Madrid the chance to move four points clear at the top of the table if they can overcome Getafe at home, a formidable lead with five games left.
Atletico advanced 4-2 on aggregate in the round of 16, thanks to two goals by Marcos Llorente in extra time and another by fellow substitute Alvaro Morata.
Messi's strike saw Barca return to the top of the standings with 31 points after 14 games, ahead of Real Madrid on goal difference, while Atletico were left in sixth spot on 25 points, having played one match more than the two pacesetters.
Unbeaten Real are a point ahead of promoted Granada and Atletico Madrid after Diego Simeone's side failed to break down their well-drilled local rivals.
Real Madrid climbed to the top of the standings with 14 points from six games, one point and one place ahead of Atletico Madrid, whom they face on Saturday in the derby at the Wanda Metropolitano.
The Argentinian playmaker's withdrawal will be a major concern for Barca, particularly given this was Messi's first start of the season after just recovering from a niggling calf injury sustained at the start of August.
Barca won a penalty early in the second half when Luis Suarez was fouled and Messi converted to put the league leaders in front and the Uruguayan forward made sure of the points with a simple finish from close range in the 82nd minute.
Atletico Madrid took a huge advantage in their heavyweight Champions League last-16 tie with Juventus, earning a 2-0 home win.
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