The team made the announcement before flying to New Jersey but did not disclose what rule was broken.
Sources say Whitehead was late to meetings Saturday morning before team departure.
Whitehead has been the Cowboys' primary kick and punt returner this season. He has returned 10 kickoffs for a 23.8-yard average with a long of 33. He has also averaged 8.8 yards per punt return with a long of 39. He has caught two passes for 40 yards and has 86 yards on eight carries on jet sweeps.
The Cowboys would likely turn to Cole Beasley and Lance Dunbar to handle the punt and kickoff duties against the Giants. Dez Bryant is always an option for punt returns but has not been used in that role since 2012.