Referee Jason Whiteley provided the pivotal moment of an untidy game when he dismissed Blues defender Paul Linwood on the half hour mark.
Before he flashed his red card, there had been little to raise the temperatures of the sparse 1,736 crowd on a bitter afternoon.
Mr Whiteley adjuged Linwood to have been the last men when the centre half hauled down Dan Holman. His decision bewildered most inside the Swansway Chester Stadium, although there were some who felt the official made the right call.
Holman smashed his first free kick into the wall but Mr Whiteley handed him a chance to redeem himself, penalising Ashley Williams for encroachment. Holman dispatched his second effort into the back of the net with the help of a cruel deflection and the visitors led 1-0.
Holman added a fine second shortly before the hour mark to condemn the 10-men Blues to another disillusioning defeat.
Neil Young hinted he was prepared to be ruthless with his selection following the woeful FA Trophy exit and he certainly proved true to his word.
Teenager striker Sean Miller was thrust straight into the starting line-up and promising forward Tom Peers was named on the bench. Ashley Williams, Michael Kay and Joe Heath also came in with Kevin McIntyre, Jason Jarrett and Craig Mahon dropping to the bench and Chris Lester back with parent club Bolton Wanderers.
For half an hour, the contest was fairly forgettable. The hosts struggled for fluency in possession, often running out of ideas and having to move the ball backwards or resorting to knocking hopeful balls forward.
Braintree too were uninspiring, choosing to shift the ball up-field quickly but the tactic paid off as the visitors had the greater chances and John Danby denied Holman with a fine save on 10 minutes, acrobatically flicking his goal-bound header behind. Sean Marks should have done better when he fired over from close range and Chez Isaac went close with a powerful strike from distance.
Gareth Seddon mustered the home side's first shot on 21 minutes but his long-range effort was sliced well wide. John Rooney became more influential as the Blues appeared to be growing into the game but then came the controversial sending off.
Linwood wrestled with Holman as he tried to break clear, although the players' reaction was mooted and there appeared to be defensive cover aplenty. Mr Whiteley disagreed and produced his red card.
Once the visitors had gone in front, it was always tough to see how the Blues could get anything out of the game with 10 men, having found things hard enough with 11. Danby was in top form to deny Daniel Sparkes from close range on 38 minutes as the visitors went into the break ahead.
Sean Miller made way through Jamie Reed as the second half kicked off, the youngster unfortunate to be sacrificed for the sending off on his full debut.
Goalscoring chances were in short supply until Holman produced the most deft of finishes to put the visitors 2-0 up on 58 minutes, stepping through some nervous tackles before looping the ball into the top corner.
Young brought on Jarrett and gave Peers his debut as the Blues desperately tried to salvage something from the game.
However, while the effort and desire lacking in the loss to Barrow last weekend returned, the quality and guile the team has been searching for all season simply did not materialise.
Peers showed his promise with some neat touches and Reed saw a header roll just wide, but the visitors were never troubled and cruised to victory.
Undoubtedly the red card changed the complexion of the game and an already tough assignment became significantly more difficult when Linwood trudged off the field.
Impossible though it is to predict what might have been had the Blues had the full compliment throughout the 90 minutes, the opening half hour gave some indication.
Injuries to key players have not helped, but the harsh fact is the side does not look good enough to survive on current form and confidence has been shot to pieces.
Young knows he must strengthen and inject fresh life into his squad when the transfer window opens in January. Critical games against sides in and around the relegation zone lie ahead and two wins before the end of the year would appear to be a must, or that could be too late.
Chester FC: Danby, Kay, Linwood, Higginbotham, Turner, G Miller, Williams (Jarrett 65), Heath, Rooney, Seddon (Peers 70), S Miller (Reed 45).
Subs: McIntyre, Mahon.
Booked: Williams.
Sent off: Linwood.
Braintree Town: Hamann, Peters, Habergham, Wells, Massey, Paine, Isaac, Davis, Sparks (Daley 73), Marks (Geohaghon 84), Holman (Cox 84).
Subs: McDonald, Carney.
Goals: Holman 34, 58.
Booked: Sparkes, Davis.
Referee: Jason Whiteley (Leeds)
Attendance: 1,736
