Hatfield Colliery closed in June with the loss of 430 jobs after almost a century of production.
The short ceremony took place at the mine, near Doncaster.
John Grogan, chairman of the Hatfield Employee Benefit Trust, which has run the mine since 2013, said it was "the end of an era".
He said: "On Monday the company will be wound up in the High Court and that will represent the end of coal mining in South Yorkshire after many generations.
"In 1980 there were 50,000 miners in South Yorkshire. On Monday morning when we're in the High Court there will be none.
"We're presenting this piece of coal as a symbol of our respect for all the miners who have gone before us in South Yorkshire and helped build the economy of our country and keep the lights on for many decades."
Accepting the gift the Mayor of Doncaster Ros Jones said: "On behalf of Doncaster and South Yorkshire I'm humbled to accept this."
The only remaining deep coal mine in England, Kellingley colliery in North Yorkshire, is due to close later this year.
The last lump of coal mined in South Yorkshire has been presented to Doncaster's mayor at a ceremony marking the end of mining in the region.