You still report the wash sale loss on a Schedule D but you enter the loss in parenthesis in column (f) and then write on the line below it in column (a) "Wash Sale" and in column (f) on that line enter the amount of the loss as a positive amount.
See page 56 "How to Report" in center of page - http://www.irs.gov/pub/irs-pdf/p550.pdf
The parenthesis would be entered manually if you were preparing the form by hand. The parenthesis means it is a loss on the first line. See page D-3 of the instructions - http://www.irs.gov/pub/irs-pdf/i1040sd.pdf