A subdued performance from the Blues leaves them teetering above the relegation zone after the 10-man hosts eased to the win.
Steve Burr cut a frustrated figure on the sidelines as his side toiled, particularly in the second half.
Defeat and results elsewhere mean the Blues must take all three points when bottom club Hyde visit the Swansway Chester Stadium next weekend or else relegation will become a much more real prospect.
Burr added three new faces to his squad in the week but only one - Luke Ashworth - made the squad.
No doubt keen to build momentum after the 2-0 win over Tamworth, the manager made only one change to the starting side.
Gareth Seddon returned from illness to partner Craig Hobson up front with Jamie Menagh dropping to the bench.
Centre back Ashworth was named among the substitutes but there was no place for new signings Andy Griffin or James Caton.
Welling announced player-manager Jamie Day had signed a new contract before the game and the Wings began well.
Vasilious Karagiannis whipped a low cross into the danger zone area but the Wings forwards failed to connect.
Blues keeper Aaron Chapman made a good save on nine minutes to prevent Lee Clarke putting the home side in front after the midfielder connected with Harry Beautyman's free kick.
Chester were struggling to bring the ball under control on a difficult surface but began to grow into the game as the half wore on.
But the hosts should have taken the lead on 22 minutes when a move down the left ended with Karagiannis firing wide from 12 yards.
Chester had the better possession and had a good chance three minutes later with Paul Linwood heading wide from John Rooney's corner.
Welling were reduced to 10 men on the half hour when Jake Gallagher left Jason Jarrett in a heap with a bad tackle with referee Daniel Cook deeming the challenge fierce enough for a straight red.
Wings top scorer Ross Lafayette wasted two decent opportunities before half time, firing wide and then forcing Chapman into a save.
Chester had more of the ball but were a little pedestrian in attack with a long range Seddon half volley the only real chance but home keeper Lee Butched saved as the sides went in level.
Burr's side began the second period well and had a penalty appeal turned down on 50 minutes when Lewis Turner went to ground in the box after a good run from Craig Mahon.
Winger Mahon was becoming more involved and sent over a fine cross on 55 minutes with Seddon heading straight into Butcher's grasp.
But the hosts took the lead against the run of play three minutes later.
Tobi Sho-Silva outjumped Paul Linwood and Karagiannis guided the ball past Chapman and into the bottom corner before being booked for his celebrations and then replaced with Toby Ajala.
Burr threw on Danny Carlton and Menagh for Seddon and Hobson as the Blues looked for an equaliser.
Mahon and Turner put some teasing balls into the area but the Wings back four defended well and kept real openings to a minimum.
With the clock winding down the Blues were running out of ideas with the home side putting more and more men behind the ball.
Sho-Silva had a chance to wrap up the win with five minutes left after being put clear but lifted his shot wide with Chapman closing.
Taking off both Seddon and Hobson left the Blues light up top and the Wings never really looked like conceding.
With a minute left on the clock the home side sealed the three points with a killer second goal.
Sub Josh Wakefield stood a cross up to the back post when an unmarked Lafayette finished with aplomb, steering his volley in off the post.
Welling United: Butcher, Fazakerley, Hudson, Taylor, Williams, Beautyman (Wakefield 63), Gallagher, Karagiannis (Ajala 58) , Clarke (Healy 63), Sho-Silva, Lafayette.
Subs: Turner, Day.
Goals: Karagiannis 58, Lafayette 89.
Sent off: Gallagher.
Booked: Karagiannis, Lafayette.
Chester FC: Chapman, L Turner, Kay, Linwood, Heath, Rooney, Jarrett (N Turner 70), Bond, Mahon, Hobson (Menagh 63), Seddon (Carlton 60).
Subs: Danby, Ashworth.
Booked: Hobson, Bond, Rooney.
Referee: Daniel Cook (Portsmouth)
Attendance: 706
