The Czechs dominated possession but were undone by sloppy passing and looked like they would lose their first match in qualifying until Pilar knocked in a rebound off Latvia goalkeeper Andris Vanņins in the dying moments.
The visitors took a shock lead in the 30th minute through Aleksejs Visnakovs after Czech Jaroslav Plasil's sloppy pass was intercepted by a Latvian defender who found Visnakovs all alone and he slotted goalkeeper Petr Cech. It was the first goal in open play for the Latvians in their qualifying campaign.
The result puts the Czechs on 13 points ahead of Iceland, who have 12 after beating Kazakhstan 3-0 away earlier on Saturday.
The Czech players said the result at home against a team that has yet to win was disappointing and a missed opportunity.
“Hopefully this will be a wake-up call for us,” Czech captain Tomas Rosicky said.
Latvia, who conceded possession and sat back in defence, repeatedly closed down the Czech attacks to deny the home side any clear cut chances in the opening half.
CZECHS PRESS
The Czechs pressed at the start of the second half and almost found the equaliser in the 50th minute when David Lafata's header hit the woodwork.
Minutes later Vaclav Prochazka fired just wide.
However, Latvia almost added a second in the 87th minute when Valerijs Sabala put his shot wide of an open goal after catching Cech far off his line.
Otherwise, though, Cech was rarely bothered by the Latvia attack while the Czechs spent much of the second half lofting crosses into the area desperately looking for an equaliser.
After Pilar's late leveller the Czechs continued to push forward and almost got the winner when subsitute Tomas Necid's shot hit prone team mate Vaclav Kadlec in front of the goal.
Czech manager Pavel Vrba called it a fair result and said his players had a tough time carving out chances against Latvian defenders who were strong in the air.
“It was a huge mistake to give away that first goal,” Vrba said. “We were missing some players but that is how it is in football.
"We were counting on getting more points but it was a just result. We will get the situation under control. This is how qualifiers work.”
(Reporting by Michael Kahn,; Editing by Ken Ferris)
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