The owners of The Robin Hood in Pontefract reported that it had been handed the levy on Friday evening, but have vowed to appeal claiming they had done everything that had been asked of them.
The remaining two businesses have not been identified.
Wakefield Council said last week it was planning to visit pubs, restaurants and takeaways over the weekend after the tougher new restrictions were imposed to help stem the spread of Covid-19.
These include closing by 10pm, table service and patrons wearing masks when not seated.
In total, the council workers, accompanied by police, visited 122 businesses and claimed the majority had "worked extremely hard" to ensure the new regulations were being followed.
They said the fines were a "last resort" and the businesses have 21 days to appeal.
Coun Maureen Cummings, Wakefield Council’s cabinet member for environment, communities and poverty, said: "We appreciate that the new restrictions may not be easy for some people but we are at a pivotal point in the pandemic and we all have to step up and do what is needed, if we are to control the spread of the virus and ultimately save lives.
“With cases continuing to rise across our district, our enforcement officers and the police are out there to help protect you and your families. Please help them by following the restrictions and if they need to step in to address issues in a pub, restaurant or takeaway please let them do their jobs, without being subject to abuse.
“Now more than ever, we all have to look out for each other and a little kindness and tolerance goes a long way.”
"We will continue to offer support and help to any business that needs it but we will also take swift action against those who do not follow the rules, in order to protect our residents.
"We, and the vast majority of businesses in this district, are not prepared to risk people’s lives. To those who have not yet stepped up I urge you to get the right measures in place now and play your part at this pivotal point in managing the spread of infection.”