It means there will be no repeat of last year's final, won by Murray, between the pair. They could, instead, meet at the semi-final stage.
The defending champion is seeded to play Tomas Berdych, the man he beat in the semis last year, in the quarter-finals. Djokovic will face Juan Martin Del Potro at that stage if the seedings play out.
Murray being drawn in with Djokovic is a boost to Rafael Nadal's title chances. The in-form Spaniard, unbeaten on hardcourts this season, landed in the other half of the draw with compatriot David Ferrer his scheduled semi-final foe.
Nadal does, however, have a tough route to the last four. Five-time winner Roger Federer, seeded only seventh this year, is in his quarter which means the two could meet at the last-eight stage of a Grand Slam tournament for the first time. They have never met at the US Open.
Ferrer's scheduled opponent at that stage is Richard Gasquet in what looks the weakest quarter of the draw.
Murray will open his title defence against France's Michael Llodra. His route through the draw continues with a second-round meeting with either Victor Hanescu or Leonardo Mayer. The Wimbledon champion's first seeded opponent is due to be Juan Monaco, with Spain's Nicolas Almagro awaiting in the last 16.
Top seed Djokovic opens against Ricardas Berankis but things could get tougher in the second round where Lukas Rosol, who famously beat Nadal at Wimbledon last season, is a possible opponent. Another potential banana skin for the Serb is a meeting with Grigor Dimitrov in round three.
Nadal opens against American Ryan Harrison and again could face a tricky second-round match against recent Montreal semi-finalist Vasek Pospisil.
Fernando Verdasco is due to be the 2010 winner's first seeded opponent and a last-16 clash with John Isner, the man Nadal beat in the Cincinnati final on Sunday, is also a possibility.
Then could come the showdown with Federer, the pair having recently played out a mini-classic in the last eight in Cincinnati.
Federer will open his bid for a sixth Flushing Meadows title against Grega Zemlja.