D'Arcy rejoined his Ireland team-mates at the start of the week after receiving treatment at a rehabilitation centre in Poland and was hopeful of making the starting line-up.
However, the Leinster midfielder suffered a setback during training on Tuesday and was withdrawn from the session with coach Eddie O'Sullivan confirming he has no chance of facing the World Cup holders in Dublin.
O'Sullivan said: "Gordon is not right yet. He has not been comfortable in training and there was no point taking a risk with him.
"His recovery will take longer than we thought - there's nothing sinister in it."
The injury is now threatening to affect D'Arcy's place on the Lions tour to New Zealand, as he struggles to impose himself on this year's Six Nations tournament.
Shane Horgan continues at inside centre in D'Arcy's absence and will partner Brian O'Driscoll in midfield after the Ireland skipper continued to train without suffering any adverse reaction to his hamstring problem.
O'Sullivan added: "Brian looked fine in training yesterday and was fine today. We will take a look at him over the next couple of days but all the indications at the moment suggest he will be fine."
O'Driscoll is the only change to the team which romped to victory at Murrayfield, with Ulster centre Kevin Maggs moving to the bench and Harlequins' Gavin Duffy dropping out of the squad altogether.