Earlier on Friday, Japan twice fought back from a goal down to overcome hosts Qatar 3-2 in an entertaining match at the Al Gharafa Stadium to set up a semi-final with South Korea or Iran.
"I think in Tashkent 30 million people are very happy because Uzbekistan are through," coach Vadim Abramov told reporters.
"From the first time I came to a press conference here I said Uzbekistan could win this tournament - no change," Abramov muttered under his bushy moustache.
Both teams were looking to make the last four for the first time and their nerves coupled with the nine changes the two sides made between them to their starting line-ups could have been the reason for a drab, scrappy opening half.
Bakaev, making his first appearance in the tournament as one of five Uzbek changes, sparked the game in to life in the opening 60 seconds of the second half when he stole away from his marker to knock in a free kick from Server Djeparov with his shoulder.
Four minutes later it was 2-0 after Bakaev again reacted quicker than the Jordan defence to convert Jasur Khasanov's cross from the left.
ACCIDENTAL CLASH
Jordan hit back when captain Bashar Bani Yaseen, who appeared to lose some teeth in an accidental clash in the first half, smashed the ball home from close range in the 58th minute after Uzbek goalkeeper Ignatiy Nesterov parried a close-range header.
Nesterov, who received lengthy treatment in the first half after a clash with his own player, left the field shortly after Jordan's goal and substitute keeper Temur Juraev did well to block Ahmad Abdelhalim's shot soon after entering the field.
Roared on by a noisy, mostly Jordanian contingent in the 16,073 crowd, the team from the Middle East pushed for an equaliser while the Uzbeks looked rattled and uncharacteristically gave away possession frequently.
The Uzbeks recovered though and they were the side most likely to score again in the latter stages.
"I have to admit fatigue and exhaustion were there," said Jordan's Iraqi coach Adnan Hamad.
"We are missing players and this influenced our performance (but) we have exited with our heads held high."
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