Batsman Kevin Pietersen was included in the 16-man Test squad despite still recovering from the Achilles tendon operation which sidelined him for part of the Ashes series victory over Australia.
Three uncapped players were named in the Test squad, Surrey wicketkeeper Steven Davies, Yorkshire leg-spinner Adil Rashid and Sussex all-rounder Luke Wright.
Seamer Liam Plunkett was recalled to the test squad for the first time since 2007 at the expense of his Durham team mate Harmison who has taken 226 wickets 63 tests and was the world's top-ranked bowler in 2004.
Harmison, 30, took three wickets in Australia's second innings in the deciding final Ashes Test and excelled for Durham last season but selector Geoff Miller said he did not merit a place against the world's top-ranked side at Test level.
"Stephen Harmison has not been included in the Test squad because we feel his form has not been consistent enough over the past 12 months to justify a regular place in the side and we want to give an opportunity to other players to make a case for selection," Miller said in an England and Wales Cricket Board (ECB) statement.
Bopara became only the fifth Englishman to notch up three consecutive Test centuries during the back-to-back series against West Indies this year and seemed to have earned the pivotal number three slot in the side.
CONFIDENCE VANISHED
However, his form and confidence vanished against Australia and he managed a top score of only 45 before being left out of the final Test at the Oval.
"It's tough," Miller told reporters. "Some great players have been through that situation where they've started well and then gone through a tough time and then gone away and resurrected their techniques and come back and I've no doubt that Ravi will be on of those. He's a quality player."
Panesar's reputation as a match-winner has been on the wane since he burst on to the scene in India in 2006 and he was dropped after the first drawn Test against Australia in Cardiff.
"Monty Panesar has struggled to find his best form this summer but he will play domestic first-class cricket in South Africa over the winter and we will continue to monitor his progress closely," Miller said.
With Andrew Flintoff now retired from Test cricket and unavailable for the one-day squad because of knee surgery, Miller said it was a chance for somebody to fill the hole left by the all-rounder.
"While we do not see Luke Wright as a like for like replacement for Andrew, we are excited by the way in which his all-round game continues to develop and believe he can make an impact at Test level," Miller said.
South Africa-born Pietersen is expected to join up with the squad after the Twenty20 internationals and should be available for the one-day series which starts on November 20.
England's first match in the four-Test series against the world's top-ranked test playing country begins on December 16 at Centurion.
England won their last Test series in South Africa 2-1 but lost at home to Graeme Smith's side in 2008.
Test squad:
Andrew Strauss (Captain), Alastair Cook, James Anderson, Ian Bell, Stuart Broad, Paul Collingwood, Steven Davies, Graham Onions, Kevin Pietersen, Liam Plunkett, Matt Prior, Adil Rashid, Ryan Sidebottom, Graeme Swann, Jonathan Trott, Luke Wright
One-day squad
Andrew Strauss (Captain), James Anderson, Tim Bresnan, Stuart Broad, Paul Collingwood, Alastair Cook, Joe Denly, Sajid Mahmood, Eoin Morgan, Graham Onions, Kevin Pietersen, Matt Prior, Adil Rashid, Graeme Swann, Jonathan Trott, Luke Wright
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