64-year-old Mr Joti, who was the chief secretary of Gujarat when Prime Minister Narendra Modi was the chief minister, will take over as the head of the Election Commission on July 6, a notification issued by the law ministry said.
Mr Zaidi will demit office tomorrow.
Mr Joti, a 1975-batch Indian Administrative Service (IAS) officer, had joined the three-member poll panel as an election commissioner on May 8, 2015 and would be in office till January 17 next year.
He retired as the Gujarat chief secretary in January 2013.
A CEC or an EC can have a tenure of six years or hold office till the age of 65 years, whichever is earlier.
He was also the secretary in the industry, revenue and water supply departments in the state.
The government is also soon expected to appoint one more Election Commissioner to fill up the vacancy caused by Mr Zaidi's retirement.
Om Prakash Rawat is the other election commissioner in the poll panel.