Peyper's performance during the Lions' semi-final win over the Wellington Hurricanes drew howls of condemnation in rugby-mad New Zealand, where pundits were scathing of his decision to sin-bin flyhalf Beauden Barrett for a ruck infringement.
The Lions were trailing 29-22 at Ellis Park when the brilliant All Black was penalised and scored 17 unanswered points while he was off the field before closing out a 44-29 win.
Peyper is generally acknowledged as one of the world's top referees and SANZAAR pointedly defended his selection.
"This merit-based policy was reflected with the appointment last year of New Zealand official Glen Jackson to referee the Hurricanes versus Lions final in Wellington," SANZAAR's South Africa-born CEO Andy Marinos, a former Wales centre, said in a statement on Tuesday.
"SANZAAR stands behind the policy and believes the best referees should be available to officiate the best matches."
Peyper's appointment sparked fresh criticism from New Zealand media.
"Wow. Sanzaar appoints Jaco Peyper to referee Super Rugby final. This really is an organisation with its head in the sand," Fairfax Media rugby writer Marc Hinton tweeted.
Local media were already up in arms over the competition's convoluted playoffs system, which saw both the Hurricanes and Waikato Chiefs play away quarter-finals despite having a superior regular season record to their opponents.
(Reporting by Ian Ransom in Melbourne; Editing by John O'Brien)
