A poor game that was ultimately decided by a goalkeeping error, saw Charlton only stay out of the relegation zone on goal difference.
To add insult to injury, Rhoys Wiggins was sent off late on.
Injury and illness caused havoc with Chris Powell’s goalkeeping options. Ben Hamer did not travel after injuring his ankle in training on Thursday.
The bug that has been affecting the players recently, struck Ben Alnwick down on the morning of the match.
Yohann Thuram-Ulien made his debut and Dillon Phillips made his first appearance on the bench. Powell will be hoping that Alnwick makes a speedy recovery as Thuram-Ulien is ineligible for the Oxford replay.
Chris Solly was again not risked, so Lawrie Wilson dropped back into defence.
Jordan Cousins and Callum Harriott flanked a triumvirate of Dale Stephens, Jordan Cousins and Johnnie Jackson in midfield.
Yann Kermorgant ploughed a lone furrow up front, and there was a bench spot for recent arrival, Astrid Ajdarevic.
Marvin Emnes had a couple of early sighters that thundered into the side netting, before Emmanuel Ledesma gave Boro the lead in bizarre circumstances after 16 minutes. His speculative long range effort lacked power but bounced in front of Thuram and deceived the keeper to end up in the back of the net.
A minute before the half-hour mark, Rhys Williams tried his luck from the edge of the box and had his effort unorthodoxically saved by Thuram’s feet.
Powell switched to a 4-4-2 formation after the break, with Jordan Cook partnering Kermorgant up front and Dale Stephens switching to the right.
Midway through the half, Powell made a double substitution, Simon Church and Danny Green, replacing Cook and Jackson.
There was a late appearance for Ajdarevic, who showed plenty of promise.
After a decidedly ordinary first half, Thuram had a much better second period.
The Addicks did get the ball in the net after 70 minutes when a deep cross from Green was hooked back by Kermorgant for Church to bundle home. The effort was ruled out for a foul on Shay Given though.
To complete a dismal afternoon, Rhoys Wiggins was red carded for a two footed lunge on Dean Whitehead.
Wiggins will miss the cup games at Oxford and Huddersfield, as well as the vital league game at Doncaster in ten days time. If Charlton lose to Oxford in Tuesday’s replay, Wiggins will miss the game at Wigan on 1 February instead.
Charlton: Thuram-Ulien; Wilson, Morrison, Wood, Wiggins; Cook (Church 67), Stephens, Cousins (Ajdarevic 76), Jackson (Green 67), Harriott; Kermorgant.
Subs (not used): Phillips, Evina, Dervite, Hughes.
Sending off: Wiggins 84 (serious foul play).
Middlesbrough: Given; Varga, Ayala, Williams R, Friend; Ledesma, Leadbitter, Whitehead, Carayol ( Kamara 88); Emnes (Jutkiewicz 57), Main (Smallwood 79).
Subs (not used): Konstantopoulos, Butterfield, Gibson, Woodgate.
Booked: Ledesma 81 (foul), Whitehead 82 (foul), Ayala 90 (foul on Kermorgant).
Goal: Ledesma (16).
Referee: Keith Stroud (Hampshire).
Attn: 14,548 (258 Charlton).