A crowd of 3,494 watched the game at the Lookers Vauxhall Stadium, which ended in a 1-0 victory for Tranmere with James Norwood netting the winner from the penalty spot .
Cheshire Police worked in partnership with Cheshire West and Chester Council , British Transport Police, Merseyside Police and businesses in planning for the game.
The Chronicle understands almost 200 officers were involved in the policing operation. Having confirmed the match passed without incident and no arrests were made, officers have thanked both sets of fans for their cooperation.
"I am pleased with the success of the police operation," said chief inspector Paul Williams from Chester Local Policing Unit.
"Our aim had always been to see the game pass peacefully whilst taking into account the rights of the people of Chester to go about their normal business.
"I would like to thank local residents and businesses for patience and understanding for any disruption that was caused. I would also like to thank the fans for their cooperation."
Supporters of both clubs had voiced their frustrations over the arrangements for game, which was switched to a 12 noon on Sunday for its original slot at 3pm on Saturday, in the lead up.
Pubs and bars in Chester were restricted selling alcohol on the morning of the game and a group of home fans unfurled a banner before kick-off protesting against the decision to move the all-ticket match.
Tranmere were allocated 1,100 tickets for the game, which sold out in three days, meaning many Rovers fans who wanted to attend the match missed out.
A section of Chester supporters have also expressed frustration over the stadium capacity being reduced for the game for safety reasons.
In September, Tranmere claimed a 2-0 win over the Blues at Prenton Park in front of a crowd of more than 7,000 with goals from Liam Hogan and James Norwood.
That was the first time the two clubs had faced each other in a competitive fixture for 24 years and Merseyside Police dealt with 'several small outbreaks of disorder' outside the ground.
A small number of people were ejected from the match, including one man who encroached onto the pitch, and two men from Wallasey were subsequently banned from attending football matches after admitting racist chanting during the match.