Pravin Rao, currently chief operating officer, will become interim CEO, India's second largest software services exporter said in a statement.
Sikka, 50, a former German IT major SAP executive who was appointed CEO and MD of USD 10 billion revenue company three years back, will become executive vice-chairman until a new MD and CEO is hired.
While the permanent replacement is to be hired no later than March 31, 2018, Sikka will focus on strategic matters and draw an annual salary of USD 1.
In a letter to the Infosys board, Sikka said the "continuous stream of distractions and disruptions" that became increasingly personal and negative, forcing him to quit.
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Without naming anyone, he said "false, baseless, malicious and increasingly personal attacks" have been made over the last many quarters and these allegations have been repeatedly proven false by multiple independent investigations.
"But despite this, the attacks continue, and worse still, amplified by the very people from whom we all expected the most steadfast support in this great transformation," he said.
Also, an anonymous letter was sent to the Securities and Exchange Board of India and the US Securities and Exchange Commission earlier this year, alleging that the Israel-based Panaya acquisition was overvalued and that some Infosys executives may have benefited from the deal.
While an independent probe absolved the board of any wrong doing, Murthy kept the pressure on making the full contents of the investigation report public.
Sikka said addressing this "noise" has consumed hundreds of hours of his time in recent times and therefore, he came to the decision to quit.
"The board denounces the critics who have amplified and sought to further promote demonstrably false allegations, which have harmed employee morale and contributed to the loss of the company's valued CEO," Infosys said in a statement.