World Cup-bound Australia proved too much for bottom-placed Indonesia in muggy Brisbane, defender Mark Milligan scoring his first international goal in the 1-0 win.
Pim Verbeek's side, which featured mostly domestic A-League players, controlled the match for long periods but proved wasteful in front of goal.
"We should have scored a few more goals to make everybody happy, but my job was to qualify for the World Cup, and to qualify for the Asian Cup, and we've done that now," Verbeek told reporters.
Kuwait joined pool winners Australia in qualifying from Group B after they eked out a 0-0 draw away to Oman in Muscat.
The 1980 Asian Cup winners needed only a point to qualify and survived some difficult moments with goalkeeper Nawaf Al Khaldi producing a number of top quality saves, including from Khalifa Ayil in the second minute of stoppage time.
Jordan became the 16th and final side through to the finals when they beat Singapore 2-1 at home and Thailand lost to Group E winners Iran 1-0 in Tehran.
Jordan, who started the day bottom of the group, overcame a dogged display by Singapore goalkeeper Lionel Lewis to finish in second place ahead of the two south east Asian sides.
Jordan striker Odai Al-Saify opened the scoring for the home side at a blustery King Abdullah Stadium after just nine minutes when he headed home from 12 metres and Al Bani Yaseen nodded the winner from three metres out in the 58th minute.
The game was briefly interrupted in stoppage time when a handful of home fans came onto the edge of the pitch following the news of Iran's late winner.
"Our achievement tonight is a gift to his Highness the King and to all the Jordanian people," coach Adnan Hamad said. "This win is a big achievement for our national team as we were so far behind in the qualifiers."
The return of their European-based players helped three-times Asian champions Japan ease the pressure on under-fire coach Takeshi Okada with a 2-0 victory over Bahrain to win Group A.
Both teams had already booked their place at the finals in Qatar but Japan were under pressure to produce a victory after a number of lacklustre performances recently.
"I was never worried about the team," Okada told reporters. "We knew there would be no excuses tonight and we got the result we deserved."
In other matches Syria thrashed Lebanon 4-0 at home to leapfrog already-qualified China to win Group D with the United Arab Emirates beating Uzbekistan 1-0 to win Group C in a battle of two Qatar-bound teams.
