The big central defender capitalised on Przemyslaw Kazimierczak's 23rd minute error by firing home a close-range left-foot volley.
And from then on, Linwood was quite happy to slip back into the centre of defence to perform his usual duties with total ease.
Kazimierczak failed to collect a deep Kevin Sandwith's free-kick, and was helpless to prevent the ball nestling in the back of the net.
Sandwith's distribution from open play and set-pieces meant that he was the best player on display in this dour League Two clash.
His searching crosses tested Stanley's brittle defence all afternoon.
But despite that, Chester did not play fantastic football themselves though the home side's horror show meant they were completely dominant throughout.
Stanley even failed to produce an effort on goal until the 65th minute and Paul Mullin tamely headed into the hands of John Danby.
John Coleman gave debuts to three of his four deadline day signings - Przemyslaw Kazimierczak, Stuart Fleetwood and Tony Grant - and Stanley lacked any kind of fluidity.
Substitute Andy Mangan however could have rescued the hosts when he fired wide during the closing stages.
Sandwith, Alex Meechan, and Roberto Martinez all had chances to double Chester's tally in the second half.
Sandwith and Martinez both had chances cleared off the line by Stanley right-back Phil Edwards, while sub Meechan had the best of the second-half chances.
He sprung Stanley's offside trap to find himself one-on-one with the keeper but could only fire against the Bolton loan-man's legs.
In the end Chester left East Lancashire with three points and the reward of doing the double over the side that came up from the Conference last season.