The expected home victories left the Uzbeks and Koreans as favourites to claim the two qualifying berths with closest challengers Iran three points back.
Japan's shock loss left the situation in Group B more complicated.
Australia were expected to ease past Oman in Sydney, but they were forced to fight back from 2-0 down and grab a 2-2 draw which meant Japan only needed to avoid defeat to become the first side to qualify for Brazil.
The pressure proved too much, however, and poor finishing, slack marking and an inspired Jordan team condemned the Japanese to their first loss in the group as the home side secured a 2-1 victory.
That lifted the West Asians from bottom to second in the group on seven points, six behind Japan and one above Australia and Oman. They are well placed to reach their first World Cup.
"This was a historic win for Jordanian football," coach Adnan Hamad told reporters after targeting four points from their final two games.
A rare failure for Japan only added spice to their next qualifier at home to Australia in June. They looked sharp for long periods in Amman but the absence of playmaker Keisuke Honda and a top-notch striker became all too apparent in a frantic finale.
"We played well, controlled the game and created many chances but we were not lucky and we couldn't score except for the once," coach Alberto Zaccheroni told reporters.
"Jordan were lucky today and they scored two goals from the few chances that they had in the game."
Japan's arch-rivals South Korea believe they have found a striking prodigy who could prove the envy of the Japanese, with 20-year-old Son Heung-min coming off the bench to pounce with almost the last kick of the game to deny Qatar a draw.
The Hamburg forward showed a few rusty touches as well as some neat dribbles in his 15-minute cameo but the crowd anticipation that greeted his every touch added fresh rigour to a Korean side struggling to unlock Qatar.
"I was amazed that Son Heung-min showed his great ability as a soccer player in only 15 minutes and I expect a lot from him for the remaining games and he will grow stronger," a relieved Korean coach Choi Kang-hee said.
Choi will hope his poster-boy forward can grow as strong as Uzbekistan playmaker Server Djeparov who was once again the match-winner for the central Asians.
The twice Asian Player-of-the-Year matched Son's scrappy goal with one of his own, a left-foot shot taking a decisive deflection off a Lebanese defender to settle the match in Tashkent.
Like Uzbekistan, Oman have never qualified for a World Cup and many expected their challenge to take a decisive blow in Sydney away from their hot and humid home in Muscat.
But Paul Le Guen's team took their chances to take a 2-0 lead before the Socceroos regrouped and sent a wave of crosses into the visitors' area to scramble a draw and leave the sides level on points.
Le Guen was disappointed but not as much as the home fans who booed their team for long periods to increase the pressure on coach Holger Osieck.
"We passed backwards, we delayed our game, there was no penetration, there was no quick ball up into the centre, so we basically played to their strengths," the German bemoaned.