Nets General Manager Billy King said the search for a new coach would begin immediately.
"The Nets ownership would like to express thanks to Avery for his efforts and to wish him every success in the future," said Brooklyn Nets principal owner Mikhail Prokhorov.
Johnson was in his third season as the Nets' coach. The team was a combined 46-102 in his first two seasons.
The Nets, in the first season at their new home in New York after 45 years in New Jersey as members of the ABA and then the NBA, are 14-14 overall but 3-7 in their last 10 games.
Johnson previously coached Dallas for more than three seasons, helping the Mavericks to the NBA Finals in 2006. His overall coaching record is 254-186.