Liverpool and Everton fans will be unable to attend games at Anfield and Goodison Park after the city was put into Tier 3.
The clubs were the only two in the Premier League who were admitting fans following changes to the Tier rules but will now have to play all of their games behind closed doors until further notice following the latest government update.
The city of Liverpool had been in Tier 2 of the coronavirus restrictions since December 2.
The new Tiers across the country mean that all games in the Premier League and Football League will now take place without fans in attendance.
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In his briefing on Wednesday afternoon, Health Secretary Matt Hancock stated that three-quarters of England will be in Tier 4 by Thursday morning.
He said: "Even in most areas not moving into Tier 4, cases are rising too, and it is therefore necessary to apply Tier 3 measures more broadly too - including in Liverpool and North Yorkshire. The rest of Yorkshire remains in Tier 3. These changes will take effect from 00:01 tomorrow morning."
Metro mayor for the Liverpool City Region Steve Rotheram said: "Despite our area leading on many of the medical developments in the fight against Covid, we have seen transmission rates rise recently in every part of our city region, leading to a worrying uptick in positive cases.
"At the same time cases have risen at alarming rates across the rest of the country, threatening to push our NHS to its limits.
"Being placed into Tier 3 today is something that none of us wanted but I hope that these new measures help to slow down and contain the spread of the virus quickly."
An Everton FC statement said: "We can confirm that, following the Government's announcement the Liverpool City Region is moving into Tier Three of the national COVID-19 restrictions from midnight tonight, we won't be able to welcome fans to Goodison until further notice, including Friday's game with West Ham."
Despite the latest restrictions and rising cases, the Premier League has announced it has "no plans" to pause the season and "continues to have confidence in its Covid-19 protocols to enable fixtures to be played as scheduled".
A statement read: "The Premier League has not discussed pausing the season and has no plans to do so.
"The League continues to have confidence in its COVID-19 protocols to enable fixtures to be played as scheduled, and these protocols continue to have the full backing of Government.
"With the health of players and staff the priority, the League is also fully supportive of how clubs are implementing the protocols and rules."
Although no club has brought the proposal to the league, West Brom boss Sam Allardyce has called for a pause to the campaign to try to reduce the number of cases.
"When I listen to the news the variant virus transmits quicker than the original virus [so] we can only do the right thing which is have a circuit break," Allardyce said after his side's 5-0 defeat by Leeds.
However, Manchester United counterpart Ole Gunnar Solskjaer questioned the logistical implications on completing the already congested season if the campaign were to be paused.
"I can't see the benefit in having a circuit break, whatever it's going to be called," Solskjaer said.
"Because when are we going to play the games? We all know this year is so difficult, but I don't think stopping the games is going to make a big, big change."
The English Football League will conduct widespread coronavirus testing with all 72 clubs next week.
The measure, planned before the rise in cases across the country this week, will see a full round of mandatory tests rolled out, commencing January 4.
More than 40 games have been called off in the EFL in the last month due to coronavirus circumstances, with nine more matches postponed on Tuesday night.
The EFL, unlike the Premier League, does not test its players regularly but relies on them reporting symptoms and on contract tracing.
NWCL suspends season until further notice
Following Wednesday's announcement regarding more stringent Tier restrictions, the North West Counties League (NWCL) decided to suspend all fixtures until further notice.
With the region placed in Tiers Three and Four, league chairman Paul Lawler emailed all member clubs on Wednesday evening, saying: "For the avoidance of doubt, non-elite sport is not allowed at all, either the playing of matches or training and players cannot travel into or out of T4.
"At this moment in time we will not be setting any dates on when or if we will resume again but I will begin consulting with clubs in due course to ascertain their opinions on a way forward.
"It is a disappointing end to a very difficult year but the health and wellbeing over all concerned has to be the priority."