The unexpected surge by the Liberal Democrats shaved Labour's majority to just five in a night of high drama which also saw Hull's first Asian councillor elected.
Labour Group secretary Chris Sumpton and veteran Labour councillor Terry Geraghty both lost their seats.
Liberal Democrat group leader Mike Ross said: "We are seven up and I put this down to the tremendous support from residents across the city who recognise the hard work and dedication of Liberal Democrat councillors.
"We are winning as far apart as Pickering Road and Bransholme and it shows that the Labour party in this city has taken many communities in the city for granted for too long."
Deputy Labour group leader Daren Hale said: "The Liberals were saying some weeks ago there was a serious risk of them taking control.
"The new boundary map does not lie and Labour is still significantly the largest party in Hull.
"We are delighted with our strong showing."
Aneesa Akbar, 26, said it was an "immense honour and privilege" to be Hull's first Asian councillor, after being elected for Labour in the Central ward.
Miss Akbar, who studied politics at Hull University and works for social landlord Sanctuary Housing, said people could not have been kinder since she had moved to the city from Manchester.
She said: "I think Hull is moving in the right direction in terms of tolerance and openness."
Conservative group leader Coun John Fareham paid tribute to the Hull Lib Dems' "amazing resilience."
"When they aren't doing that well nationally they seem to buck the trend in Hull. Here they are resurgent again."
Council leader Steve Brady said the result was a "message from the electorate that they are happy with the way the city has moved over the last few years and they want us to carry on with the plans for the future."
Coun Brady - who had a thumping majority in his Southcoates ward - said the city had seen Â£3.5bn investment in the past four years, adding: "We intend to carry on, I don't regret one decision we have taken as a Labour authority in all the investments we have put in. They were right for the city and give hope and inspire our young people."
Traditionally Hull has had low turnouts and last night was no exception with an overall turnout of 25 per cent. One ward, North Carr saw just 14.6 per cent.
Retiring Labour councillor Martin Mancey said he would welcome Australian-style compulsory voting.
"Otherwise it becomes too whimsical," he said. "I think it's very sad people don't recognise the impact of registering their opinion."
*The final tally was Labour 31 seats, Liberal Democrats 24 and Conservatives 2.
The number of seats have reduced from 59 to 57 as a result of boundary changes.