"Marius should not have been involved given that he was a member of the match official team for the weekend's match," the sport's governing body said in a statement while accepting responsibility for what it called an "oversight".
South African Van der Westhuizen was at England's training session at Pennyhill Park on Tuesday and although he received a vote of confidence from Ireland coach Joe Schmidt, World Rugby said it took the decision "to avoid any additional unfair and unnecessary conjecture".
"Marius is an outstanding talent with a big international future and both he and his employer SARU (South African Rugby Union) fully support the decision," the statement added.
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Ireland, already crowned Six Nations champions, will complete the grand slam for the third time if they beat England at Twickenham on Saturday.
(Reporting by Simon Jennings in Bengaluru, editing by Ed Osmond)
