Yanev, who replaced Martin Petrov in the 86th minute, scored off a free kick in the three minutes of injury time.
Bulgaria had opened the scoring in the first minute when Svetslav Todorov netted a Yordan Todorov pass, beating defender Yuji Nakazawa.
Japan had their chances soon afterwards, but Yuki Abe's shot was saved by the Bulgarian keeper in the 16th minute, and Keiji Tamada's lightning shot hit the right post in the 24th minute.
Yasuhito Endo missed a couple of shots on a corner in the 35th and 36th minutes.
Former Feyenoord midfielder Shinji Ono and Mitsuo Ogasawara came in to galvanize the Japanese attack in the 61st minute.
Ono fired a pass to give Ogasawara a close-range shot which went wide in the 70th.
An effort by Alessandro Santos was saved by the keeper and Keiji Tamada's shot following an Ono pass missed in the 81st minute.
Forward Seiichiro Maki finally found the net, collecting a rebound and striking home off a defender in the 76th minute. But Japanese hopes of victory were extinguished by Yanev.
“We played not so bad, we played rather well overall. We created so many scoring chances and still we lost due to an early goal and a late goal.
“We received a slap in the face in the end,” said Japan coach Zico.
“We must score a goal whenever we create a chance. That's football.”
Bulgaria will play Scotland in Kobe on Thursday, followed by a Japan-Scotland match on Saturday in Saitama in the three-nation tournament.—AFP