Loose forward du Toit was named player of the year, Springboks coach Rassie Erasmus was named coach of the year and the Springboks were crowned team of the year for the first time since 2009.
Du Toit was the first Springbok recipient since Bryan Habana in 2007 and third overall.
He received the award ahead of five other nominees in Wales captain Alun Wyn Jones, England flanker Tom Curry, New Zealand flanker Ardie Savea, South Africa team-mate Cheslin Kolbe and United States hooker Joe Taufete'e.
English outside back Emily Scarratt won the women's player of the year award.
She beat four other nominees in England team-mates Sarah Bern and Katy Daley-Mclean, France halfback Pauline Bourdon and New Zealand halfback Kendra Cocksedge.
French back Romain Ntamack was named as breakthrough player of year.
Fijian playmaker Jerry Tuwai was named the sevens men's player of the year while new Zealand's Ruby Tui was named women's sevens player of the year.
Wayne Barnes received he referee of the year award.
All Black halfback TJ Perenara was awarded the try of the year. His effort to squeeze over in the corner following some great work beforehand against Namibia was a real stunner.
Former Irish No 8 Jamie Heaslip was given a special merit award for his work on and off the field for the Ireland and British and Irish Lions team.