Japan came into the match on the back of three wins from three under new coach Hajime Moriyasu but they could not maintain their perfect record as they continue preparations for the AFC Asian Cup in the United Arab Emirates, beginning January 5.
In an entertaining first half in which both teams looked to attack, the visitors' best chance fell for on-loan Newcastle United striker Salomon Rondon after 11 minutes.
Rondon slipped his shot under Japan goalkeeper Daniel Schmidt only for defender Takehiro Tomiyasu to race back and scrape the ball off the line with a sliding lunge.
After the diminutive Shoya Nakajima had missed two good chances for Japan, he turned provider five minutes before half-time as they opened the scoring.
His whipped, deep free-kick was met by the late-arriving Sakai to score with a flying volley that Venezuela keeper Rafael Romo could not keep out at his near post.
It was the Marseille defender’s first goal in 49 appearances for his country.
Japan have traditionally been built on a solid defensive foundation, yet it is the attacking verve under Moriyasu that is most impressive.
Nakajima and Salzburg’s Takumi Minamino, who has scored four times in six appearances for the Samurai Blue, were threatening throughout behind solo striker Yuya Osako.
Yet after Nakajima and Osako were taken off midway through the second half, the tempo dropped and Venezuela battled back into the game.
They were rewarded for their perseverance when Sakai went from hero to villain, bundling substitute Luis Gonzalez to the floor with a clumsy challenge to give away the penalty 10 minutes from time.
Rincon calmly dispatched the penalty, sending debutant goalkeeper Schmidt the wrong way.
There was late drama when Japan captain Maya Yoshida thought he had clinched the win with a header in injury-time, only for it to be correctly ruled out for offside.
Japan were late arriving to the Oita Dome due to heavy traffic coming to the stadium and there were plenty of empty seats to start the match as supporters were also held up.
Moriyasu said after the match that a police escort was needed to get the coach to the stadium ahead of kick-off.
This is a potentially worrying sign for next year’s Rugby World Cup as Oita will host six games, including two quarter-finals.
The 40,000 capacity Oita Dome is almost 10 kilometres outside the city centre.
Moriyasu’s side have one final match to prepare for the Asian Cup, facing Kyrgyzstan on Tuesday.
