Three times the Blues led, three times defensive lapses allowed Boro to draw level and prevent the 10-men hosts taking the three points.
Eight minutes into the game, referee Ben Toner dismissed Jason Jarrett for the kind of challenge that used to be called over enthusiastic but now considered dangerous.
Goals from John Rooney, Matty Taylor and Ross Killock looked to have earned the gutsy Blues the win, but Boro replied through Louis Moult and two-goal Andy Brown, who ensure the game ended level four minutes from time.
Nuneaton will feel like this was a point gained and the home side will view this more as two points lost. Defensive improvements are a must, but it is hard to be critical after a performance filled with guts and endeavour.
Blues boss Steve Burr - who flew out to Jordan with the England C squad following the match - made one enforced change from the 4-3 win over Tamworth.
On-loan defender Matty Brown failed a pre-game fitness test, meaning new boy Ricky Bridge - signed from Newcastle Town on Friday - came into left back and Paul Linwood moved into the middle alongside Killock.
With Brown ruled out, Burr named Nathan Turner - missing since the 2-2 draw with Hereford United in November - on the bench.
Key men James Armson and top scorer Moult had been in doubt for Nuneaton but the pair were included in the visitors line up.
After a scrappy opening, the game came alive on eight minutes when the hosts were reduced to 10-men.
Jason Jarrett tried to bring the ball under control in midfield but his touch was heavy and referee Ben Toner deemed his challenge on Adam Walker worth of a red card.
His decision left the home fans fuming but Jarrett did appear to go over the top of the ball, although Walker looked to have the same thing in mind.
Rather than retreat, the Blues dug in and found the best possible response when Rooney opened the scoring on 16 minutes.
Rampaging right back Lewis Turner nipped past Theo Street and curled his cross back to Rooney, who steered the ball in off the post.
Rooney forced Boro keeper James Belshaw into a save from 25 yards but the attacking midfielder failed to get hold of his shot.
Nuneaton centre back Gavin Cowan then came close to heading a Rooney free kick into his own net as the home side pressed.
Boro came back with Blues keeper Aaron Chapman getting down well to keep out a Brown drive and racing off his line to keep out Wes York after a good ball from Armson.
Chapman could not prevent the equaliser from arriving on 32 minutes as York crossed from the right and Moult headed home from close range, although Burr will feel his defenders should have done better.
Parity lasted only four minutes with in-form striker Taylor putting the hosts back in front, poking home after jinking winger Craig Mahon whipped over a cross from the left and ball bounced back off the inside of the post.
Gareth Seddon put Taylor clear minutes later but he flashed high and wide from a tight angle before Chapman denied Brown at the other end.
As good as the Blues have looked going forward in the past few weeks, defensive worries persist and the visitors took full advantage to level on the stroke of half time.
York floated another cross over from the left and Brown sent another close range header into the back of the net.
There could be few arguments that the Blues deserved to go into the break ahead and Boro will have been grateful for such charitable defending.
Compared to the opening 45 minutes, the second half proved pretty tame.
Nuneaton had more of the ball and looked to build pressure, but struggled in the main to create clear opportunities.
Big centre half Gareth Dean came closest, having a header cleared off the line after Chapman had failed to deal with a corner.
Boro threatened from set pieces and the Blues survived a couple of nervy moments but began to get back into the contest.
Rooney saw his free kick from 25 yards deflected inches over the bar and Belshaw punched a looping Linwood header clear under pressure.
Heading into the final 20 minutes, the breakthrough came as Seddon challenged for a Rooney corner and the ball fell to Killock, who smashed home from 10 yards.
Nuneaton threw on centre forward Dave Hibbert and he forced Chapman into a save with a curling shot as the visitors pushed hard.
Boro dominated the closing stages and the nervous Blues backline cracked four minutes from time, failing to deal with a corner and allowing Brown to fire home his second and ensure the points were shared.
Chester FC: Chapman, Turner, Killock, Linwood, Bridge (N Turner 70), Rooney, Bond, Jarrett, Mahon, M Taylor, Seddon.
Subs: Danby, Lindfield, Menagh, Daniels.
Goals: Rooney 16, M Taylor 36, Killock 69.
Sent off: Jarrett.
Booked: N Turner.
Nuneaton Town: Belshaw, Streete, Cowan, Dean, Gordon (HIbbert 73), Sleath, Walker, Armson, York, Brown, Moult.
Subs: Delfouneso, Trainer, C Taylor, Adams.
Goals: Moult 32, Brown 45 and 86.
Referee: Ben Toner (Darwen)
Attendance: 2,214.
