The hosts looked like they were heading for victory when the Argentinian's unexpected departure forced Rangers to finish the game with ten men, but the R's kept going and managed to grab a decisive leveller.
Neil Warnock made five changes to the R's side that lost 2-1 against Norwich last weekend, with Radek Cerny, Fitz Hall, Tommy Smith, DJ Campbell, and Federico Macheda all coming into the starting XI at stadiummk..
The R's lined up in a 4-4-2 formation, with Hill, Gabbidon, Hall and Young making up the defensive line.
With captain Joey Barton suspended following his red card against the Canaries, Faurlin wore the skipper's armband and joined Shaun Derry in central midfield, with Mackie on the left and Smith starting on the right flank.
Macheda, making his first start since his loan arrival from Manchester United, was joined in attack by DJ Campbell, himself making his first appearance in the starting XI since our opening day fixture against Bolton.
After a disappointing run of results in the Premier League, QPR came into this match looking to get back to winning ways and, in doing so, end a disastrous run of 11 years without an FA Cup triumph.
QPR began brightly, with DJ Campbell almost releasing Mackie with a clever back heel but Dons centreback Gary Mackenzie was on hand to clear the danger.
More than 5,000 travelling QPR fans made themselves heard from the off, and Macke nearly gave them something to cheer on six minutes. Tommy Smith played a delightful ball overt the Dons backline but Mackie's effort from 16 yards flew over the bar.
But three minutes later the hosts thought they had taken the lead when Daniel Powell's cross-field effort found the bottom corner but the referee's assistant ruled it out for offside.
Buoyed by that, Karl Robinson's men went close again moments later with Dean Bowditch's powerful drive from 18 yards which flashed wide.
Macheda and Smith were working hard to develop an understanding and the early signs of this game were certainly encouraging as they consistently looked to combine.
MK Dons were certainly providing a stiff test for the R's in front of a packed stadiummk, and in the 21st minute Lewington released Jabo Ibehre down the left side and onto the edge of the R's penalty area.
When many expected him to shoot, Ibehre squared for Luke Chadwick but Cerny comfortably smothered inside the six-yard box.
The travelling Hoops reacted with a strong chant of "Come on you R's," and Faurlin almost responded immediately with a free-kick from 25 yards. The effort itself seemed to be a comfortable take for Dons custodian David Martin, but he fumbled at the first attempt but quickly gathered with the R's unable to take advantage.
On 26 minutes the hosts had a strong claim for a penalty dismissed by referee Michael Oliver. Powell's cross from the right seemed to hit the arm of Hill as he attempted to block the centre.
Clearly the man in the middle deemed it as ball-to-arm, to the frustration of Robinson in the technical area.
In an entertaining affair, moments later DJ Campbell had the ball in the back of the Dons net but his cool finish was also ruled out by the referee's assistant. His reaction as the ball rolled into the net was one of a man who knew he had strayed into an offside position.
It was very evident that neither team wanted their objectives in the league impacted on by an FA Cup replay, as both sides sought to win the fixture. It made for a very open game with chances at both ends.
Macheda almost picked out the on-rushing Young at the far post with an excellent cross-field ball on 38 minutes but the R's full-back was unable to get the vital touch as the delivery bounced out of play.
After the re-start both teams continued to press and play an open game. Macheda twice stood up great centres from the left byline, the first evaded everyone while Campbell so nearly diverted the second goalwards.
QPR certainly moved up a gear in the second period, and enjoyed a sustained spell of possession with Macheda a real menace down the left side.
But on 64 minutes it was the hosts who took the lead.
Shaun Williams' cross from the right side was brought down by Heidar Helguson in the area but as the Icelandic striker looked to clear he was dispossessed by Bowditch who slammed into the far corner from 12 yards.
Rangers had a chance to get back on level terms through Smith in the 70th minute.
Young got down the right flank and played a delightful cross into the centre but the R's forward headed wide from eight yards.
Moments later Jay Bothroyd was introduced to the fray for Macheda and the substitute almost levelled but saw his header go inches wide from Smith's cross.
With ten minutes remaining, Faurlin went down clutching his knee after he stretched to intercept a stray pass. Warnock stood in the technical area with his head in his hands as a stretcher was called for.
Judging by the reaction of the QPR players who surrounded the fallen skipper, it would appear the injury is a serious one, although we await further details to confirm this.
Twelve months ago it was Mackie who left the pitch with a serious problem in this competition at Blackburn, and now the R's are left to curse another unfortunate injury.
As Faurlin was carried off the pitch, he received a standing ovation from both sets of fans who recognised the potential seriousness of the injury.
Having already used his allocation of substitutes, it meant Warnock had to watch his team finish the game with only ten men.
Incredibly, it didn't stop Rangers from getting themselves back into the game in incredible fashion with three minutes remaining.
Following a clearance from the back, Helguson raced through to be met by the out-rushing Martin who was unable to get a clean connection on the ball, but collided with Helguson who went to ground with the ball still in play.
The R's No22 reacted quickest and got himself up in time to slam the ball into an empty net from the edge of the area, to the delight of the QPR fans gathered behind the goal.
There were five minutes' added time at the end, but Rangers held firm and will now welcome MK Dons to Loftus Road for a replay later this month.