After Ruan Pienaar had missed two relatively easy penalty opportunities in the 48th and 52nd minutes, Jones extended the Lions half time lead with a penalty in the 59th minute but then Bryan Habana scored a cracking try that replacement Morne Steyn converted to leave four points separating the sides.
Steyn was again on the mark in the 68th minute to make it a one point game but Jones cancelled that out from the restart after Schalk Burger - lucky to be on the field after an early first half incident - had been penalised for offside.
Then, following consultation with the TMO, Jaque Fourie was awarded a try after touching down in the right hand corner with Steyn's (Morne) touchline conversion leaving the Boks three in front.
Jones' penalty looked like sending the series right down to the wire but then O'Gara was harshly adjudged to have tackled Fourie du Preez as he gathered O'Gara's high kick and Steyn landed the 54 metre kick to win the game.
And the series.
Lions: Robert Kearney; Tommy Bowe, Brian O'Driscoll, Jamie Roberts, Luke Fitzgerald; Stephen Jones, Mike Phillips; Gethin Jenkins, Matthew Rees, Adam Jones, 4 Simon Shaw, Paul O'Connell capt, Tom Croft, David Wallace, Jamie Heaslip. Replacements: Ross Ford Andrew Sheridan, A-W Jones, Martyn Williams, Harry Ellis, Ronan O'Gara, S Williams.
South Africa: Frans Steyn; JP Pietersen, Adi Jacobs, Jean de Villiers, Bryan Habana; Ruan Pienaar, Fourie du Preez; Tendai Mtawarira, Bismarck du Plessis, John Smit; Bakkies Botha,Victor Matfield; Schalk Burger, Juan Smith, Pierre Spies. Replacements: Chiliboy Ralepelle, Deon Carstens, Andries Bekker, Danie Rossouw, Heinrich Brussow, Jaque Fourie, Morne Steyn.