The 37-year-old Mangini was called by Johnson one of the league's up-and-coming coaches, but he went 23-26 in three seasons in his first head coaching job. He had another year remaining on his contract.
"For the current New York Jets organization, we've made the decision to move on," Johnson said. "It's a judgment call."
Mangini held a team meeting yesterday morning to say farewell.
"I appreciate the opportunity that Woody and [GM] Mike [Tannenbaum] gave me for the past three years as the head coach of the New York Jets," Mangini said in a statement. "The organization has terrific people and I wish the Jets nothing but success. The time and effort invested by the coaches and players was tremendous and I value that beyond words.
"We worked hard to achieve two winning seasons out of the past three. I regret that we could not reach our goals for this year. I will always appreciate the passion and support of the fans as our focus was trying to build them a championship-caliber foundation and team."
"I feel that we let him down and we could have done a better job of making plays," wide receiver Jerricho Cotchery said. "It's tough."
The Jets went 1-4 in their final five games, losing to Denver, San Francisco, Seattle, and Miami and barely beating Buffalo.
They did not reach the postseason for the second straight year despite an offseason spending spree that included a trade for Favre after his retirement and return at Green Bay.
The 39-year-old Favre had just two TD passes and nine interceptions in those final five games.
Favre led the league in interceptions with 22 and complained after Sunday's 24-17 loss to Miami of pain in his right shoulder and neck.
The win gave the Dolphins the AFC East title under Chad Pennington, the Jets' longtime quarterback who was cut when the team obtained Favre.
As a rookie coach, Mangini took a team that had been 4-12 the previous year to the playoffs with a 10-6 record in 2006 and earned the nickname "Mangenius" from the tabloids. However, the Jets went 4-12 last season.
