(CNN) -- A penalty save from Jordan goalkeeper Amer Sabbah prevented Japan from becoming the first country to qualify for the 2014 FIFA World Cup in Brazil.
Japan needed just a draw in Jordan to secure passage to a fifth consecutive World Cup after Australia had earlier been held by Oman.
But Alberto Zaccheroni's Asian champions trailed after Khalil Bani Ateyah and Ahmad Ibrahim scored either side of half time to give Jordan a 2-0 lead.
Manchester United playmaker Shinji Kagawa pulled one back for Japan before Yasuhito Endo of Gamba Osaka saw his spot kick turned around the post by Sabbah with 18 minutes remaining.
Japan still hold a six-point lead over Jordan, who moved from bottom to second, at the top of Asian qualifying Group B and the Blue Samurai will secure a place at next year's finals if they avoid defeat against Australia in June.
The Asian campaign sees the top two teams from each of the two five-country groups advance to the World Cup, with both third-placed teams entering a playoff.
The winner of that two-legged tie plays the fifth-placed team from the South American section to decide who goes to the tournament.
A late goal from Brett Holman helped Australia maintain their challenge for the second automatic qualification spot in Group B.
Australia trailed Oman, who have won just once in six qualifiers, 2-0 before New York Red Bulls midfielder Tim Cahill halved the deficit when heading home from a Luke Wilkshere corner.
The draw left Australia in third position, level with Oman after picking up six points from five matches, and one point behind Jordan having played a game less.
Uzbekistan remain on course to reach the World Cup for the first time after a 1-0 win against Lebanon in Tashkent.
A 63rd-minute goal from captain Server Djeparov moved Uzbekistan onto 11 points at the top of Group A, with Mirjalol Qosimov's team one point ahead of South Korea having played one more game.
Substitute Song Heung-min had earlier scored a 96th-minute winner as South Korea came from 1-0 down to beat Qatar 2-1.
Lee Keunho put South Korea ahead at the Seoul World Cup Stadium before Khalfan Al Khalfan equalized for the 2022 World Cup hosts.
South Korea's last-gasp winner left Choi Kang-Hee's side three points ahead of third-placed Iran, with both teams having played five matches.
In the African qualifying zone, Egypt's bid to reach their first World Cup since 1990 received a major boost as the Pharaohs struck late to beat Zimbabwe 2-1 and go five points clear in Group G.
After midfielder Hosny Abd Rabou gave the home side the lead midway through the second half, Knowledge Musona struck from distance to bring the visitors level.
But with time running out, Mohamed Salah was tripped inside the box, allowing Mohamed Abou Trika to score from the penalty spot with just two minutes left.
The game was also significant for the entry of 10,000 fans into the stadium to watch the game, with recent Egypt matches having been played behind closed doors because of security concerns.
American coach Bob Bradley's side boast nine points from their first three matches in Group G, with only the winner going through to the third and final round of African qualifying later this year.