"The company has today [Monday] announced that Makhudu Sefara, editor of The Star, has left the company with immediate effect," deputy executive chairman Tony Howard said in a statement.
"The parting of ways between Makhudu and Independent Media SA was amicable and mutually agreed upon."
Howard said Sefara, having worked for the company previously, returned in 2009.
Sefara was the editor at the Saturday Star before being appointed editor of The Star.
"He very ably led The Star for more than two years and was recently called upon to oversee difficult but necessary changes at the paper, a task he successfully completed with grace and sensitivity," Howard said.
The company and Sefara could not agree on how best to use Sefara's talents further in the company.
"As a consequence, Makhudu and the company agreed on a separation agreement that was amicable and about which they are not prepared to comment on any further," Howard said.
The Star's deputy editor Kevin Ritchie was appointed acting editor until further notice.
Earlier on Monday, Sefara confirmed to Sapa he had stepped down.
"I have stepped down and I am no longer the newspaper's editor, it was an amicable departure," Sefara said.
There had been editorial changes and resignations by senior staff at Independent Newspapers since Iqbal Surve's Sekunjalo-led consortium bought the company last year.
Last week, The Mercury editor Philani Mgwaba resigned. Mgwaba had been editing the newspaper since 2012.
Former Sunday Independent editor Moshoeshoe Monare joined the Mail & Guardian as deputy editor in March. He had replaced Sefara at the Sunday Independent after became The Star's editor.
In February, veteran financial journalist Ann Crotty resigned from Business Report, the Independent Newspapers' financial daily. Crotty joined weekly newspaper, the Sunday Times.
Last year, Cape Times editor Alide Dasnois was fired after the newspaper published a front-page article on Public Protector Thuli Madonsela's finding against Agriculture, Forestry and Fisheries Minister Tina Joemat-Pettersson.
It found the minister was guilty of maladministration and improper and unethical conduct in the awarding of an R800 million tender to a Sekunjalo subsidiary to manage the state's fishery vessels.
Surve denied that Dasnois's dismissal was due to the fisheries tender story.
Dasnois has since approached the Commission for Conciliation, Mediation and Arbitration.
Surve reportedly walked out at the Nat Nakasa Awards ceremony two weeks ago after Dasnois received the award for courageous journalism.
Deputy President Cyril Ramaphosa gave a speech at the event.
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