The visitors made the worst possible start, falling behind in the second minute when Ahmed Al Binali turned Atsuto Uchida’s cross into his own net.
Ali Yahya levelled from the penalty spot eight minutes after the interval but the result left the AFC Asian Cup 2011 hosts a point adrift of third-placed Bahrain after their final Group A game.
Japan sealed qualification for South Africa with a 1-0 win in Uzbekistan last Saturday and they enjoyed a dream start, taking the lead on their first attack just 90 seconds into the match.
Shunsuke Nakamura played the ball towards the right flank where Uchida took advantage of a slip by Majdi Abdulla to burst clear.
He tried to pick out Shinji Okazaki in the box but Al Binali got to the ball ahead of the striker and deflected it past goalkeeper Qasem Burhan.
Japan should have made it 2-0 in the ninth minute when a low cross by Keiji Tamada was spilled by Burhan at the feet of Okazaki, who fired wide from six yards.
Qatar wasted an opportunity to draw level a minute later when an unmarked Majdi Abdullah headed wide.
Japan went close again on the half-hour mark when Yasuyuki Konno’s cutback from the left byline found Hideo Hashimoto, whose back-heel trickled agonisingly past the far post.
Qatar should have levelled, though, in the 41st minute when Yuki Abe gave away possession in the centre circle to Magid Mohammed, who brought the ball forward before laying it off to his left to an unmarked Mohammed Abdulraab but he fired just wide of the far post.
Japan had the ball in the net again a minute before half-time but Tulio’s effort was disallowed following a handball by Tamada.
Qatar continued to press after the break and they were rewarded in the 53rd minute when referee Subkhiddin Salleh pointed to the spot after Magid had his shirt tugged by Yuji Nakazawa as the pair chased a ball into the Japan box.
Yahya sent Narazaki the wrong way from the spot to level matters.
Qatar continued to threaten on the break and Yahya nearly capitalised in the 73rd minute, firing over from the edge of the box after the ball was pulled back to him by Yusef Ahmed.
But the home side had the better of the late opportunities with Okazaki heading wide in the 81st minute before substitute Keisuke Honda shot over a minute from time.