The Blue Samurai and Czechs had both failed to break down Peru in the two previous games before Chelsea goalkeeper Cech ensured the winner-takes-all clash in Yokohama also finished in a stalemate.
"Nowhere in the world could a team improve as much in so little time as we have," Japan coach Alberto Zaccheroni told reporters, slightly overcooking his praise after another tepid performance. "This team has tremendous potential."
Cech brilliantly saved a Shinji Okazaki header after 78 minutes before acrobatically blocking Tadanari Lee's follow-up from point-blank range, drawing gasps from a crowd of 65,000.
"The fact we didn't score in the two games is something to chew over," said midfielder Keisuke Honda after Japan had gone a record 14th match unbeaten at home.
"We need to play with a bit more intensity and take our chances."
The home side were playing their first competitive games since winning a record fourth Asian Cup in January and March's deadly earthquake and tsunami in northeast Japan.
"If we can't beat teams like this at home we won't scare too many of the world's top teams," said Japan captain Makoto Hasebe.
"We were poor," added the German-based midfielder, though Japan played marginally better than against Peru last week. "There is room for improvement still. I apologise if we were boring."
"Japan were quality opponents," said Czech coach Michal Bilek. "We were missing some of our regular starters so I was a bit worried but the younger players coped well."
