With the game locked at 1-1 with 25 minutes remaining and Kuwait threatening, Djeparov took advantage of space on the edge of the area to fire a first-time, left-foot shot which curled away from a diving Yaqoub Al Taher in the Kuwait goal.
The result put Uzbekistan on six points in Group A after their second win of the tournament and left Kuwait on the brink of an early exit.
"Our game is very good. I'm very happy we beat Kuwait today and I think we can make a surprise," coach Vadim Abramov said after equalling their tournament best quarter-finals appearances in 2004 and 2007.
"If my team can qualify for the semi-finals that will be a very good result for us."
An entertaining second-half was in mark contrast to a drab first, which was witnessed by just 3,481 fans at the 22,000 capacity Al Gharafa Stadium on another chilly early evening in Doha.
The Uzbeks enjoyed the best of the first-half, producing a number of neat, short passing moves but, lacking pace in attack, they came to nothing.
They took the lead, however, four minutes before the interval in fortunate circumstances when Maksim Shatskikh's 22-metre free kick took a big deflection off a team mate.
The 32-year-old struck a curling right-foot effort which struck the back of a ducking Azizbek Haydarov, who was making a nuisance of himself in the defensive wall, which diverted the ball past a befuddled Al Taher.
"That's two goals from a deflection, maybe sometimes your team needs a little luck," Kuwait coach Goran Tufegdzic bemoaned, referring to the first goal they conceded to China in their opening match.
Kuwait began the second half in a much brighter, energetic fashion with substitute Hamad Nayef going very close with a glancing header within 90 seconds of the restart before earning his team a penalty minutes later.
The diminutive striker was brought down by a needless challenge from Anzur Ismailov on the edge of the area and Bader Al Mutwa sent Uzbek keeper Ignatiy Nesterov the wrong way from the penalty spot.
The equaliser brought the game to life and both sides had chances to take the lead before Djeparov, who was always a threat playing just off striker Alexander Geynrikh, struck the winner which was deserving of a bigger audience.