Ros Jones’s party lost four seats from 2017 – three to the Conservatives and one to Edlington & Warmsworth First.
But Labour gained one seat in Rossington & Bawtry from Independent John Cooke.
The Conservatives gained a seat in Bessacarr, Norton & Askern and Stainforth & Barnby Dun.
They also went tantalisingly close in Hatfield but lost to Labour by 28 votes.
Localist group, Mexborough First, again returned three councillors to represent the town with a big majority despite a strong effort on the campaign trail from Labour.
Former Labour member Rob Reid also took a seat from his former party in the Edlington & Warmsworth ward under the Edlington & Warmsworth First banner.
Despite losing seats, Labour didn’t experience big losses in Doncaster in so-called ‘Red Wall’ areas unlike places in the Midlands and North East.
Labour now have 40 seats, the Conservatives 11, Mexborough First three and Edlington & Warmsworth First one.
The ruling party saw quite a high turnover of candidates and 18 of Labour 40 candidates were elected for the first time.
Speaking after being elected for a third term as Doncaster’s elected mayor, Ros Jones said: “I’m delighted that the people of our borough have shown confidence in me, delivering for our town.
“We’ve got a 10 year strategy to really kick the borough, it’s not one, three, four years because we have a long-term vision to drive this borough forward.
“It’s also about our towns and villages and that’s why we’ve brought forward our new master plans to be there to deliver for the people.
“We want to deliver a new hospital which we started in excess of three years ago.”
When asked about Labour’s result in Doncaster compared to poor outcomes elsewhere in the country, Mayor Jones added: “In Doncaster, we show that we deliver for our people and work with them and I’m delighted they have shown confidence in us.”
Labour will see a raft of new councillors heading to Civic Office after a number of previous members decided not to stand again or who were not chosen this time around.
On the new crop of councillors, Jones said: “We’ve got a fantastic bunch of councillors that have been elected, some returning and some new faces who are young and will inject huge enthusiasm into local politics to work for the better of our borough.
“We’ve got a great blend of maturity and youth coming together to deliver for everyone.”