A 1-1 second-leg draw left the tie level at 2-2 on aggregate and after extra-time ended goalless it was the visitors who held their nerve to keep their dreams of a debut at the FIFA World Cup alive, winning the shootout 9-8.
Anzur Ismailov opened the scoring for the hosts with a close-range finish after Jordan goalkeeper Amer Sabbah had failed to deal with a free-kick.
Uzbekistan dominated much of the play but their lead was cancelled out by Saeed Al Murjan's wonder strike from long distance just before the break.
The home side seized the initiative inside the opening five minutes, Ismailov reacting quickest to poke home when Sabbah could only parry a free-kick into the defender's path.
But Jordan equalised just before the break as Al Murjan controlled the ball 30 yards from goal and unleashed a dipping volley that Murotjon Zukhurov could not get to.
They continued to threaten on the counter-attack after the break but Mirjalol Qosimov's side posed the greater threat - especially from set-pieces.
