Efforts to leave come just two days after both were announced as two of six English clubs to sign up to the controversial new competition.
The ESL has been widely criticised since being announced on Sunday.
Around 1,000 fans gathered outside Chelsea’s Stamford Bridge home ground before their game against Brighton on Tuesday to protest their involvement.
Chelsea and City were part of English football’s ‘big six’ clubs – alongside Arsenal, Liverpool, Manchester United and Tottenham – to have agreed to join the new league.
In total, 12 European clubs announced their intentions to form the breakaway league, which they hoped to establish as a new midweek competition.
It was condemned by football authorities and government ministers in the UK and across Europe by UEFA and leagues associations.
Chelsea were the first club to indicate they will not press ahead by preparing documentation to withdrawn. City withdrew soon after.
Chelsea and City were not drivers of this plan, they were the last to sign and feared being left behind.
It is not clear how easy it is or how binding the contracts are.
The decision to try have Chelsea leave was taken by owner Roman Abramovich and the club’s board board after witnessing negative global reaction to the Super League.
There was a fear that it could do reputational damage to the club and undermine some of its campaigning and community work.
Questions were raised internally as to whether fans would respond to the club if it continued with a proposal which has gone down so badly.
The decision was made earlier on Tuesday before protests started outside Stamford Bridge.
Earlier in the day, UK Prime Minister Boris Johnson met with the Football Association, Premier League officials and fans’ representatives, after which the government said it will take “whatever action necessary”, including legislative options, to ensure the proposals were stopped.
Johnson’s stance is supported by Labour and the Liberal Democrats.
A statement released after a meeting between the Premier League and the 14 clubs not involved said they “unanimously and vigorously” rejected plans for the competition.
It added that it is considering “all actions available” to stop the competition and asked the six teams to end their involvement immediately.
Former Chelsea winger Pat Nevin on BBC Radio 5 Live
I’m not even mildly surprised – it didn’t look like Chelsea wanted to get on that train but they didn’t want to be left at the station.
I don’t think these clubs were prepared for anything. This seems like utter panic from a set of clubs. I think this is the first break that falls and then we are back into something like normality.
Chelsea wanted to move stadium a few years ago, fans weren’t having it. The club, instead of pushing it through, said “we were wrong”. They can change, they can adapt.
It’s gone now, dead in the water. It is that big because the other clubs would look a bit silly without them now.