An Adam Sumner free-kick was mishandled by Clitheroe keeper Chris Thompson to give the Blues the lead but Bradley Knox looked to have stolen two points with seven minutes remaining.
Gavin Clark popped up however to steer home the winner on a ground which hasn’t brought the Dolly Blues much luck in recent years.
Since 2010 they have only picked up four points from six visits to their Lancashire neighbours, including a tough defeat last August having come from two goals down to lose 4-2.
On this cold evening where slipping and sliding was recurrent, it was looking like any point would be a good one and a mistake would likely decide the game.
Clitheroe looked nervy at the back but dangerous down either side with Stavros Tserpes and Dimitri Tuanzabe always liable to cause danger on the break.
Brad Carroll had the first effort from a 30-yard free kick that bounced before Mike Hale and smashed off the post.
At the other end, a neat one-two between Preston loanee Dylan Davidson and Jordan Connerton ended with Davidson, on his first start for City, miscuing straight at Thompson.
Craig Carney then fired over from a good position and Jacob Gregory cut inside from the right after a good run before slicing way off target.
Sure enough it a mistake that broke the deadlock in first half added time. Sumner’s deep free-kick from the right was met but fumbled by Thompson and the ball dropped into the net, in what is perhaps one for the dubious goals panel.
The Clitheroe stopper somewhat redeemed himself early on in the second period, keeping out Connerton’s flick on after a corner hadn’t been dealt with.
The striker then nearly turned provider but Billy Akrigg was inches from converting his fizzed centre on the slide.
Midway through the half Clitheroe had a good spell, first Tuanzabe failed to convert Tom Williams’ cutback before Knox was denied by the on-rushing Hale. Tom Carroll could then not hit the target from outside the box from the resultant corner.
Pressure but no conviction from City meant the game reached the 83rd minute before Knox got through one or two more challenges than he should have done and scuffed past Hale into the bottom corner to level.
The Blues came back though and with a minute remaining Ryan Winder, who made his Lancaster return on the hour mark, forced a top save from Thompson before Robbie Bromley brilliantly denied McKenna tucking in the rebound.
Just into stoppage time McKenna was felled 10 yards inside the Clitheroe half and Sumner whipped in a menacing ball, Clark rising highest and glancing into the corner to cap a fine start to the season for the whole-hearted defender.
The game was far from finished though as Hale had to be on his toes to change direction after Carroll’s shot took a ricochet.
Lancaster held on though to arrest their mini-dip in form and move up to fourth in the table.
Lancaster City: Hale, Henry, Westwood, Clark, Sumner, Gregory (McKenna), Akrigg (Winder), Wills, Carney, Davidson, Connerton.