Whitehead, one of Town's most consistent performers under Gary Peters, was shown two yellow cards during a match-long tussle with Northampton's Scott McGleish.
Peters has accepted the decision, and hopes that his Town replacement will help the side pick up points.
He told the Shropshire Star: "It will definitely cost him his place on Saturday and let's hope it costs him his place for the rest of the season because that means Shrewsbury Town will have won a few games without him and will be doing well."
Whitehead would have only been banned for one match, but a pre-season sending off means the ban is doubled. Whitehead's discipline has otherwise been excellent this term, picking up only four other yellows for the entire season.
It is likely that Andy Wilkinson will revert to full-back to cover Whitehead's absence, with Darren Tinson and Dave Walton in the centre of defence.