Uzbekistan's Anzur Ismailov missed the decisive spot kick as Jordan won the shootout 9-8 after the second leg tie had ended 1-1 and 2-2 on aggregate at Tashkent's Pakhtakor Stadium.
Jordan coach Hossam Hassan's team now go through to another playoff in November against the fifth-placed South American side, currently Uruguay, for a World Cup berth.
Hassan had called it the most important game in Jordan's football history but the visitors, who lost all four away games in the group stage, were a goal down after five minutes.
Anzur Ismailov put the hosts ahead, slotting home after Jordan goalkeeper Amer Sabbah had saved Server Djeparov's freekick from just outside the box.
Saeed Al Murjan equalised for Jordan against the run of play with a spectacular 25-metre half-volley just before halftime.
The second half was a tame affair with Uzbekistan having the upper hand but failing to find the net, with Sanjar Tursanov missing a good chance when he fired over from inside the area in the 59th minute.
Extra-time was marred by a floodlight malfunction that led to 15 minutes of stoppage time being played.
Australia, Iran, Japan and South Korea have already booked the four automatic berths from Asia for the 2014 finals.
- Sports & Recreation
- Hossam Hassan
- Anzur Ismailov