Seigo Narazaki brilliantly saved Yang Hao's spot-kick to salvage a point for the hosts but the result will increase the mounting pressure on Japan coach Takeshi Okada.
The Blue Samurai were once again booed from the pitch in freezing Tokyo after a similar reaction to their 0-0 draw with Venezuela in a home friendly this week.
"We have to accept the jeering," Okada told reporters. "Improving the team is my job and I think we have improved.
"We created several chances and defensively we were very solid. The booing we have to use to motivate us."
Japan's best chance came in the 54th minute when right back Atsuto Uchida smashed a shot against the post after a strong run but moments later China were almost gifted the lead.
Rong Hao's cross from the left was spilled by Narazaki and almost dribbled over the line before defender Tulio dived in to hook the ball clear.
CLOSE SHAVE
Striker Yoshito Okubo's late volley was blocked as the Japanese were sparked into life by their penalty escape but Okada's side again lacked a cutting edge.
China could have been in front by half-time after Rong's fierce blast shaved the post in the 33rd minute.
Okada insisted Japan were the better side despite their failure to deliver any end product.
"We were very excellent at the back," said Okada, who has come under fire since his bold declaration that Japan's target at this year's World Cup in South Africa was the semi-finals.
"It's a shame we didn't get the three points but the players did well. We must make sure we get three points against Hong Kong before we play South Korea in the last game."
China coach Gao Hongbo claimed a moral victory.
"We played better football," he said. "But they hit the post and we missed a penalty so 0-0 is a fair result."
World Cup qualifiers and East Asian title holders South Korea face Hong Kong on Sunday in the second game of the four-team tournament.
