An unfortunate late own goal from Alex Whitmore saw the Blues edged out at the Gateshead International Stadium.
CJ Hamilton’s volley was turned into his own net by Burnley loanee Whitmore eight minutes from time.
The hosts, lifted by the arrival of new boss Neil Aspin, started the game well; having a goal ruled out for offside and forcing Ben Heneghan into a superb interception all in the opening five minutes.
It was a scrappy affair, and the Blues somehow did not go ahead on 18 minutes.
A superb counter attack saw Rooney switch the play to Tom Shaw, who nutmegged his marker and tore down on goal – his first shot was cleared off the line by Simon Ramsden, and his second struck the inside of the post.
Chances seem to be few and far between, Craig Baxter had a go from range for the visitors; but his low effort fizzed wide.
At the other end, Ryan Lloyd slipped Hannah in behind – but he lashed his shot wide of the far post.
Gateshead had a scrambled effort at their own end towards the conclusion of the half – resulting in Jon Worsnop doing well to block Paddy McLaughlin’s effort – before CJ Hamilton blasted over.
Nevertheless, the second half didn’t live up to expectations and chances were a massive rarity – both sides threatening but not clinical in the final third.
Heneghan nodded wide from a cross by Craig Mahon, who was making his 100th appearances for the club.
Debutant Danny Hattersley then headed straight at the keeper while in acres of space, but the Halifax loanee was offside.
CJ Hamilton, also making his debut, was lively for the hosts and his run and shot was comfortably stopped by Worsnop.
The game sprung to life in the last quarter of an hour, Worsnop making a stunning save on this occasion from a deflected Jordan Cranston effort.
A run of chances were to pay dividends – as the Heed took the lead with just eight minutes of normal time remaining.
A right wing cross was volleyed goalwards by Hamilton, and it appeared to be a sliced clearance into his own net by Alex Whitmore.
CJ Hamilton had taken the game by the scruff of the neck, smashing a shot just wide moments later that would have wrapped up the game.
Rooney then blasted a shot straight at Russell in stoppage time, leaving Chester condemned to defeat in the North East.
Gateshead: Russell, Baxter, Curtis, Clark, Shaw (Hamilton 12), Mafuta, Cranston, Bowman, Ramsden, Wrightson (Honeyman 62), McLaughlin.
Subs Not Used: MacDonald, Buddle, Smith.
Chester: Worsnop, Higgins, Heneghan, Whitmore, Hunt, George, Shaw (Chapell 86), Rooney, Lloyd (Mahon 69), Hannah, Hattersley.
Subs Not Used: Forth, Sharps, Dyson.
Scorers: Whitmore (OG) 82.
Attendance: 842 (133 away).
Referee: Jason Whiteley (Leeds).