Farrell, the former Great Britain rugby league captain, picked up the injury in an internal trial match and has already been out for a month.
Saracens boss Steve Diamond confirmed the toe is not broken - but he revealed Farrell's rugby union debut is still some way off.
"Farrell needs another two or three more weeks definitely," said Diamond.
"In layman's terms the injury is a bruised toe but in medical terms it is probably far more detailed than that.
"But it's not broken. There is a problem with the second toe, which is very painful and needs rest. He is off his feet and the toe is isolated in a boot.
"There is no point him coming back early because the injury will be there all season. We don't want to have a bloke of his abilities to be worrying about his toe.
"So we have put him on the back burner."
Farrell will miss Saracens' Guinness Premiership games away at Worcester and at home to Sale.
He may be available to play in the Anglo-Welsh Cup game against Cardiff on October 1 or against London Irish eight days later.