Earlier, on Sunday, Vaughan opted out of the fourth and final Test quoting personal reasons after stepping down from England captaincy.
Bopara will play under Kevin Pietersen, who was named on Monday as the new captain of England's Test and one-day sides.
The England selectors also announced a 15-man squad for the one-day series and two Twenty 20 matches against South Africa.
Uncapped Notts' batting all-rounder Samit Patel has been included. Sussex stumper Matt Prior earned recall.
Test: Kevin Pietersen (captain), Tim Ambrose (wk), James Anderson, Ian Bell, Ravi Bopara, Stuart Broad, Alastair Cook, Paul Collingwood, Andrew Flintoff, Steve Harmison, Monty Panesar, Ryan Sidebottom and Andrew Strauss.
ODI&T20: Kevin Pietersen (captain), James Anderson, Ian Bell, Ravi Bopara, Stuart Broad, Alastair Cook, Paul Collingwood, Andrew Flintoff, Samit Patel, Matt Prior (wk), Owais Shah, Ryan Sidebottom, Graeme Swann, Chris Tremlett and Luke Wright.