Yasuhito Endo put the Blue Samurai in front in the 14th minute at a sellout Sapporo Dome, sweeping home after a dazzling run down the right from Yuichi Komano.
Spain-based striker Miku pegged Japan back, twisting while on the ground to deftly poke the loose ball past goalkeeper Eiji Kawashima with the outside of his right boot.
"First half, [we] got early goal but should have capitalised on that, taken more chances," Japan coach Alberto Zaccheroni told reporters.
"In the second half we created a few chances but I thought our pace dropped off a bit."
Manchester United's pre-season signing Shinji Kagawa flashed a header just past the post on the hour mark. It proved costly as Miku struck moments later.
"We were at home and had lots of chances to score so I feel deeply sorry we didn't manage to win," said Kagawa. "It's really disappointing. We'll put it right for the World Cup qualifiers."
Honda praised Venezuela, who finished fourth at last year's Copa America.
"They're a tough side," said a bare-chested Honda. "They put us under a lot of pressure and didn't let us play our game. We will have to increase our work rate."
