There have been calls for D'Arcy to be dropped after he also disappointed in Ireland's opener in Rome, but Declan Kidney is expected to stick with the under-fire centre.
Irish captain Brian O'Driscoll also faced criticism for his role in the defensive lapse but Schmidt believes the two players have enough experience playing together that this was only a one-off.
"You can leave (D'Arcy) isolated because he is such a good defender - usually," said Schmidt, who previously coached Rougerie when he was backs coach at Clermont.
"He can pick two guys up very quickly. He was holding on (Damien) Traille and then breaking to Aurelien, and the relationship between D'Arcy and O'Driscoll is that they are pretty good working together no matter what sort of a system it is.
"It's just that when you are trying to play a push defence, it is hard to get your feet close enough to really get a good shoulder and grip on a big guy like Aurelien."
Meanwhile veteran Munster scrum-half Peter Stringer has been called up to the Irish squad by Kidney as cover for teammate Tomas O'Leary who has been suffering with a back spasm.