Zimmerman is the Hispanic neighborhood watchman who shot and killed unarmed black teen Trayvon Martin last month.
Zimmerman has not been charged in the incident, which has sparked protests from people who say Martin's death is the result of racial profiling.
A lawyer for Zimmerman, who has not been seen in public since the uproar began, said the neighborhood watchman shot Martin after the teen attacked him.
The altercation apparently happened after Zimmerman followed Martin because he thought the youth seemed suspicious, police have said.
Lee re-tweeted to his 250,000 followers last weekend an address posted online, supposedly of where Zimmerman has been staying.
As it turned out, the address was that of David and Elaine McClain, a couple in their 70s with no connection to the case, who say they were forced to leave their home after being threatened.
Lee, who has directed the films "Do the Right Thing," "Jungle Fever" and "Malcolm X," as well as the documentaries "When the Levees Broke" and "4 Little Girls," apologized Wednesday night on Twitter for re-tweeting the wrong address for Zimmerman.
"I Deeply Apologize To The McClain Family For Retweeting Their Address. It Was a Mistake. Please Leave The McClain's in Peace," Lee, 55, wrote. "Justice in Court."