The match started in the worst possible fashion for the Serbian as he was twice broken before Youzhny held serve to move 4-0 ahead in the opening set.
Djokovic did break back at 5-2 before holding serve to move one game behind, but the Russian held strong to serve out the opening set 6-4.
It was the world number one that bossed the second set, however, as he secured two successive breaks to send the match into a deciding set.
Djokovic broke his opponent in the opening game of the third, but Youzhny responded with a break of his own to level the match at 3-3 in the final set.
Djokovic rallied in the final moments, however, as he broke at 4-4 before serving for a spot in the next round.