Had the home side's Luke Beckett and Nick Richardson managed to find the net with any of the many opportunities afforded them by a far from composed Manchester City defence, then even a replay would have been scant reward.
"We had the chances to win and I'm disappointed for the players who gave so much only to have what is an embarrassing scoreline facing them," the Chester chairman and manager, Terry Smith, said.
"I thought we were the equal or better of Manchester City throughout the game."
As it is, Joe Royle's team live to fight another FA Cup day, but recent concerns over their shaky League form - a trio of defeats preceded their trip to the Deva Stadium - will hardly have been arrested by this low- quality performance against the Nationwide's bottom club.
"We had a few apprehensive players before the game and I hope that's settled them now because in the past couple of weeks we haven't been playing like we did earlier in the season," Royle conceded.
After a bright opening by the home side, a mix-up between the Chester goalkeeper Wayne Brown and the central defender Matt Woods allowed Shaun Goater to stab in from 10 yards.
But just eight minutes later, Manchester's defence looked equally fragile as Darren Wright slipped a pass through for Richardson to fire home from just inside the box. While the visitors showed speed and movement, only in the dying moments did they achieve anything like dominance in the danger area, and these qualities were more than matched by the determination and energy of Chester.
On either side of the interval Richardson had fine chances to put his side ahead, but his efforts from the edge of Nicky Weaver's area, both provided by Beckett, were squandered.
Weaver was forced into action twice before his side nudged ahead, each time denying Beckett, a Manchester fan, who was by some measure the best player on the day.
Having seen one header fly just wide a few moments earlier, Ian Bishop's 78th-minute effort from a whipped Richard Edghill cross gave Manchester control before a finale which flattered the visitors.
Goater converted a Kevin Horlock pass in injury time, and Horlock's next shot ricocheted beyond Brown off the unfortunate Matty Doughty.
Goals: Goater (19) 0-1; Richardson (27) 1-1; Bishop (78) 1-2; Goater (89) 1-3; Doughty (og 90) 1-4.
Chester City (5-3-2): Brown; Moss, Fisher, Woods, Doughty; Richardson, Reid, Nash (Berry, 90); D Wright (Cross, 82), Beckett. Substitutes not used: Conkie, Lancaster, Milosavijevic.
Manchester City (4-4-2): Weaver; Edghill, Wiekens, Jobson, Granville (Whitley, h-t), Pollock, Bishop, Horlock, Kennedy; Peacock, Goater. Substitutes not used: Crooks, Allsopp, Tiatto, T Wright (gk).
Referee: T Heilbron (County Durham)
Bookings: Chester: Reid. Manchester City: Horlock.
Man of the match: Beckett.
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