For the third successive game, Chester gave their opponents a two goal head start but this time the comeback attempt fell short.
But for some excellent goalkeeping from Christian Dibble, the Blues would have got something from the game but that shouldn't cover up a performance that fell below the standard set in the past few weeks.
Nuneaton gained control in the first half with two goals inside three minutes, James Armson thumping home before a deflected Lee Fowler free kick wrong footed Jon Worsnop.
Chester had to improve after the break and did, sub Craig Hobson scored within five minutes of being introduced and Dibble made some fine saves to keep the home side in front.
Boro added a third on 79 minutes through sub Marcel Barrington to ease the tension but Hobson got another with two minutes to go and Dibble had to make another excellent stop in time added from Rhys Oates to be certain of the win.
Last season the Blues lost 1-0 at Nuneaton in a dreadful match that summed up the season, lacking ideas and inspiration before giving up a cheap goal.
Things had taken a significant turn for the better since though and two wins and a draw in the last three matches reinforced the optimism on the terraces.
There were still issues to iron out, a bad habit for giving opponents a head start being one, but Steve Burr won't be too concerned if his side continue to produce comebacks like the one that saw them go two down to Da
rtford in the week before winning win 4-2.
Burr had to make one change from that game with Kingsley James suspended after picking up five bookings so Danny Harrison made his first league start since September.
Although the fixture marked the halfway point in the season, there was already more than a tinge of desperation about Nuneaton's position.
A midweek mauling down in Dover took their winless run to six games and left them eight points behind Southport in the final safe place.
Liam Daish replaced the sacked Brian Reid in the hot seat two months previous and had overhauled the squad with loans and free transfers.
He gave a debut to keeper Christian Dibble, borrowed from Barnsley to replace the injured James Wren, and Adam Dawson started having rejoined on loan from Leicester City but there was no place for captain Gareth Dean or midfielder Adam Walker.
Chester made a bright start with Craig Mahon curling wide and Dibble saving a scuffed John Rooney shot before home side went closest when Anton Brown's overhead hook rolled past the post on seven minutes.
Rooney had Dibble scrambling with a free kick from 35 yards but Boro were getting on top with right winger Dawson the main danger and took the lead on 20 minutes.
Gash was proving a handful and his knockdown sat up for James Armson, whose first time finish from 12 yards gave Jon Worsnop no chance.
Michael Kay headed wide from a corner as the Blues tried to find a response but the lead was doubled on 23 minutes after Matty Hughes bundled over Armson.
Ex-Wrexham midfielder Fowler took the free kick and his low effort wrong footed Worsnop, suggesting the ball had taken a deflection off the wall.
For the third game in a row, the Blues had given themselves a two goal mountain to climb and could have no real complaints about the scoreline.
Armson had a chance to make it three but fired straight at Worsnop and it took until 35 minutes for Chester to produce something of note when Hughes rolled Oates behind the back four but Dibble made himself big and blocked well.
Midfield was the main area of concern for the Blues without James to drive them forward but there were moments to cling to, including a fine chance before half time when Oates rounded Dibble but couldn't direct his shot on target.
Craig Hobson and Ibou Touray replaced Harrison and Gareth Roberts for the second period, and the switch paid off less than five minutes after the restart.
Oates appeared offside when he found acres of space down the right but the assistant kept his flag down and he sent over a cross that Hobson glanced past the stranded Dibble.
Hobson almost scored again a minute later, this time meeting Hughes' cross but his header flew the wrong side of the post.
Nuneaton now began to look like a team unaccustomed to being in front with Dibble using his chest to keep out Oates' thumping strike.
Dawson twice forced Worsnop into action with good strikes but the momentum of the game had shifted in the Blues favour.
Nuneaton sacrificed Onome Sodje to give them an extra man in midfield and the outstanding Dawson continued to trouble Chester down both wings.
Dibble made a good save down low to keep out a Rooney free kick on the hour and an even better one on 75 minutes, pushing out an Oates shot after Hughes' backheel put him clean through.
Had that chance been taken Nuneaton might have folded but the hosts punished the miss with a third goal four minutes later.
Dawson, the clear man of the match, swept over a low cross from the right and sub Marcel Barrington slammed home from close range.
Chester sensed the game slipping away but kept on going and were rewarded with a second on 88 minutes.
Sean McConville's corner flew across the face of goal and Hobson nodded home from two yards out at the back post.
There was time left for one more chance, Dibble making an excellent point blank save to prevent Oates finding the net and the home side clung on for the points.
Nuneaton Town: Dibble, Starosta, Streete, Charles, Franklin, Dawson, Fowler (Smith 89), Armson, Brown, Sodje (Barrington 59), Gash,
Subs: Cowan, Stankevicius, Quinn.
Goals: Armson 20, Fowler 23, Barrington 79.
Chester FC: Worsnop, Kay, Brown, Charnock, G Roberts (Touray 46), Rooney, Harrison (Hobson 46), Mahon, McConville, Hughes, Oates.
Subs: C Roberts, Peers, Menagh.
Goal: Hobson 50 and 88.
Referee: Paul Rees (Bristol)