Rafael van der Vaart put the Netherlands ahead after 12 minutes when Japan failed to clear their lines and Arjen Robben doubled the lead six minutes before half-time.
However, Alberto Zaccheroni's men responded well and were level after an hour following goals from Yuya Osako and Keisuke Honda.
The result extends the Netherlands' unbeaten record to 16 matches, while Japan have stopped the rot after back-to-back defeats.
Van der Vaart and Nigel de Jong were among five players brought into the Dutch starting XI following their final World Cup qualifier against Turkey, with striker Robin van Persie having withdrawn from the squad through toe and groin injuries earlier in the week.
Shinji Kagawa dropped to the bench in the most notable change for Japan from their 1-0 friendly defeat to Belarus in October.
Hotaru Yamaguchi blazed over the crossbar from the edge of the penalty area early on as Japan looked to gain an early advantage.
Yet it was the Netherlands who opened the scoring in the 12th minute as Van der Vaart capitalised on a dreadful Atsuto Uchida header to break clear of the Japanese defence and chip over goalkeeper Shusaku Nishikawa.
Jeremain Lens prodded just wide of the left post in the 23rd minute, drawing a last-ditch challenge from Uchida, before Robben forced a diving save from Nishikawa with an effort from 18 yards.
The Bayern Munich winger had better luck from similar range after 39 minutes as Robben curled in a wonderful left-footed strike to hand the Netherlands a comfortable lead.
However, Osako pulled one back for Japan a minute before half-time, slotting beyond Jasper Cillessen from the centre of the penalty area after some good work by Makoto Hasebe to set up the chance.
Yuto Nagatomo went close in the 55th minute as Japan dominated following the break, and they got their just reward five minutes later as Honda drove home an equaliser from inside the area following a scintillating passing move.
Kagawa almost put his side ahead in the 67th minute, but Cillessen tipped the Manchester United man's shot wide of his left-hand post.
There was a golden chance for Japan to cap a sensational comeback with 12 minutes remaining, but Yoichiro Kakitani slipped the ball narrowly wide after being put through on goal.