All six Labour seats were lost.
Labour group leader Pat O'Neil, who lost her Goole South seat, said: "For all the seats to go it is quite devastating."
She said the votes reflected on Labour's stance on Brexit adding: "We should have a definite policy on what we intend to do."
The Conservatives increased their majority by two seats, while the Liberal Democrats more than doubled the number of seats they hold to eight.
The Independents had been hoping to make massive strides in the all-out elections, but in the end also took eight seats, including in Goole South where David and Barbara Jeffreys beat two sitting Labour councillors.
Tory deputy council leader Jonathan Owen - who will be throwing his hat in the ring for the leadership of the council after council leader Steve Parnaby stepped down - said they had got their message across to voters.
Average turnout was a better-than-expected 32 per cent.
He said: "I'll be honest we started the night thinking we would be losing seats because of the national situation but then we suddenly realised that overall we had gained two in Goole North which must be a first."
Coun Owen who will be vying for the top job at the group's annual general meeting on Wednesday said: "I think we told the story we wanted to tell and people respected that.
"We think we have quite a good track record. We try and listen to people and we are quite financially sound."
Independent councillor Geraldine Mathieson who retained her Cottingham North seat said she was disappointed "that more Independents have not had a greater impact on the party vote."
Out-spoken Independent councillor Andy Strangeway lost his Pocklington Provincial seat by just 14 votes.
Overall result: Conservative 49 Liberal Democrats 8 Independents 8 Yorkshire Party 2
HULL: No change - but Labour leader issues stark warning to leadership to act on Brexit or 'get another kicking'
There was no change in Hull - Labour took one seat (Avenues) and lost one (Sutton) to the Lib Dems - retaining its majority of seven.
But Labour council leader Steve Brady had a stark warning for the Labour unless a deal is agreed with Theresa May to secure Brexit that "whenever the next election is Labour nationally will get another kicking certainly in the north of England."
There was an alarming number of spoilt votes in ballot papers with the word "Brexit" written on them.
"We are talking up to one hundred in lots of wards," he said. "The last thing Labour wants is to lose its core vote. They might be safe in the knowledge there's no general election - if there was one God help them."