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.
After their 1-1 draw in Amman on Friday, both sides remained hopeful of qualifying for the play-off game with the fifth-placed team from South America.
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.
Sabbah was lucky to survive a poor piece of handling just after the hour, the goalkeeper palming a cross into the middle of the penalty area but luckily for him a defender reached the loose ball before an Uzbek forward.
In added time, Jordan had their best opening of the half but Odai Al-Saify handled when controlling the ball, and the game headed into extra-time.
A floodlight failure saw the game delayed for 15 minutes in the first period of extra-time and both sides struggled to get going again once play resumed.
With no further goals, the tie had to be decided by penalties and the away side showed their coolness under pressure to seal a dramatic win.
