Mary Pitcaithly, convener of the Electoral Management Board for Scotland (EMB), revealed the decision following a “stakeholder” consultation.
She said the next-day count would allow last-minute postal votes to be processed without the pressure of an immediate count and enable “more effective risk management” in relation to the electronic counting system.
She added: “It will also allow more attentive scrutiny from observers and ensure that staff are operating at optimal effectiveness while making crucial decisions in the service of local democracy.”
In the last three council elections – 1999, 2003 and 2007 – there was no choice but to count votes the next day because they coincided with the Scottish Parliament elections, which had to be counted first.
Now the elections have been “de-coupled”, the count for the council elections could start immediately after the polls close on Thursday, May 3.
Politicians, including former Scottish Tory leader David McLetchie and former Edinburgh Labour Lord Provost Lesley Hinds, argued people wanted to know the result as soon as possible and said an overnight count would allow talks about the formation of the new council administration to get under way.
The EMB consultation, published just before Christmas with a closing date of January 6, was limited to election officials, the Electoral Commission, the political parties panel, the leadership of the Convention of Scottish Local Authorities and the media.
Ms Pitcaithly said the overwhelming majority of responses favoured a next-day count.
In a direction issued to her fellow returning officers, she said: “I am committed as convener of the EMB to ensure that the interests of the voter, not the dictates of systems, suppliers, logistics or other stakeholders, must drive the process.
“The voter must come before any other stakeholder, be they candidates, media, observers or electoral administrators.”