Uzbekistan midfielder Server Djeparov opened the scoring early on only for Shinji Okazaki to equalise for Japan after the break. The result leaves the sides level on four points at the top of the group after two rounds of games.
North Korea, who beat Tajikistan 1-0 earlier in the day, sit in third place on three points, with Tajikistan yet to get off the mark.
Uzbekistan started in lively fashion at the Pakhtakor stadium and had a chance for an opener in the seventh minute when midfielder Timur Kapadze hit the woodwork with a powerful shot from just outside the box.
Captain Djeparov then put the hosts in front 60 seconds later, knocking home the loose ball after the Japanese defence failed to clear Alexander Geynrikh's cross.
The Blue Samurai, who were weakened by the absence of Keisuke Honda and Kengo Nakamura, poured forward in search of an equaliser while Victor Karpenko might have made it 2-0 with a long-range shot that almost caught out Japan goalkeeper Eiji Kawashima.
Tadanari Lee then struck the post for Japan just before the interval, but Alberto Zaccheroni's side eventually pulled things level in the 65th minute, with Okazaki heading home Maja Josida's cross.
Kawashima then came to Japan's rescue with a vital save to deny Djeparov as the game ended in stalemate.