The Tories took the swing wards of Ossett and Wrenthorpe and Outwood West, the former by 600 votes.
Tony Homewood and Annemarie Glover, herself a former councillor, are the new elected members there.
But the biggest shock was in Wakefield East where the Conservative candidate Akef Akbar narrowly won following a recount.
Mr Akbar admitted he was slightly surprised to win given Labour's historic dominance of that area of the district, but promised to repay the faith shown in him by local voters.
He said: "It's a huge win, but the hard work starts now.
"Wakefield is where I was born and bred, so people know me and trust me to get things done.
"I've got so much work to do and I want to make things better for the people of Wakefield East."
Labour managed to hold Stanley and Outwood East, as well as the Horbury and South Ossett, despite Tory optimism in both areas in the week before polling day.
Labour also returned sitting councillors in Wakefield West and Wakefield North, while the Conservatives comfortably held their seat in Wakefield Rural.
Eight of the 22 seats have been declared so far, with the next batch of results expected to be announced from about 6pm.
As things stand, Labour now holds 44 of the council's 63 seats. The Conservatives now have 14 following their three gains.
Results so far
Wakefield West - Labour HOLD by 300 votes
Wakefield North - Labour HOLD by 505 votes
Wakefield East - Conservatives GAIN from Labour by 48 votes
Wakefield Rural - Conservatives HOLD by 1,440 votes
Horbury and South Ossett - Labour HOLD by 161 votes
Ossett - Conservatives GAIN from Labour by 666 votes
Stanley and Outwood East - Labour HOLD by 633 votes
Wrenthorpe and Outwood West - Conservatives GAIN from Labour by 180 votes