Prague goalkeeper Ondrej Kolar also saved shots by Messi, Gerard Pique and Sergi Roberto to deny the hosts.
Barcelona has eight points in Group F. Prague has two. Borussia Dortmund and Inter Milan both had four before their game against each other later Tuesday.
Barcelona extended its record unbeaten streak in Europe’s top club competition to 34 consecutive home matches, a run that dates back to 2013.
But some fans jeered the team for the poor showing that comes three days after Barcelona was stunned 3-1 at Levante in the Spanish league, ending a seven-game winning streak.
“When you go two games without a win (at Barcelona) the pressure is maximum,” Pique said. “We have to solve this as soon as possible. We are not playing like we would like in the Liga and the Champions League, but we are not in a bad position. We must keep our calm and improve.”
Barcelona is tied on points with Real Madrid atop the Spanish league standings.
Valverde chose Ousmane Dembele to replace the injured Luis Suárez in the starting 11 for Barcelona.
With his top striker out, Valverde altered Barcelona’s standard 4-3-3 formation and put Messi at the front of a 4-2-3-1. But other than Messi’s chances and a pair of flashes from his teammates, Prague didn’t have much trouble holding its own. Barcelona forward Antoine Griezmann, for example, was a non-factor.
Barcelona won 2-1 at Prague two weeks ago in a match that was evenly contested. And Prague coach Jindrich Trpisovsky dared to play at the Camp Nou with a very high defensive line on the road.
The tactic worked to limit Barcelona’s attack, which was mostly the same side that was upset at Levante.
Barcelona appeared to start on the right foot when Pique sent a long through ball to meet Nelson Semedo’s run down the right. But Kolar stretched his foot to deflect the right back’s shot in the 11th.
Messi’s best chance came after he ditched his marker near midfield to receive a pass, sped around two back-tracking defenders, and fired the a left-foot shot off the woodwork. Kolar then blocked another shot by Messi and a header by Pique before halftime.
Barcelona lost left back Jordi Alba, who has already been hampered by injury this season, at halftime apparently to a left leg problem. Sergio Roberto replaced him and drew a save from Kolar after Dembele had set him up with a nice chipped pass.
Kolar also denied Messi in the 77th after he was assisted by substitute Ansu Fati inside the six-yard box.
Pique will miss the next match against Dortmund on Nov. 27 for an accumulation of yellow cards after he was booked in the first half.
Source: WSP