The back row forward was cited for a spear tackle on Springbok fullback Patrick Lambie towards the end of South Africa's 49-3 victory in a Pool D clash in Wellington last Saturday.
Spear or tip tackling, where a player lifts an opponent into the air and returns them to the ground head first, is outlawed because of the potential for head injuries.
Waqaniburotu, who captained Fiji during the Pacific Nations Cup earlier this year, was spared a six-week ban because of "his admission, his excellent disciplinary record and remorse and the absence of aggravating factors", according to a statement.
The 25-year-old's World Cup is effectively over unless Fiji embark on an unlikely run to the last four as he will not be eligible to return until October 10 -- the day after the completion of the quarterfinals