The two teams had drawn a World Cup qualifier in November but it was Jordan who came out on top when Vahdat Hanonov put the ball into his own net from a set piece, ending Tajikistan's dream run in Qatar.
In a goalless opening half, Ehson Panjshanbe came closest to scoring for Tajikistan when his effort hit the bar while Jordan forward Yazan Al-Naimat failed to convert two difficult chances to break the deadlock.
But Jordan finally found the breakthrough from a corner in the 66th minute when Abdallah Nasib's header went in via a deflection off the chest of Hanonov - their goalscorer from their last-16 win over the United Arab Emirates.
Tajikistan tried their best to score an equaliser, with Alisher Shukurov coming close when he tested keeper Yazeed Abulaila from distance with an effort that stung his palms, but Jordan managed to hold on for a famous victory.
Hussein Ammouta's side will next play either 2015 champions Australia or South Korea in the first semi-final on Tuesday.
