(CNN) -- Captain Graeme Smith survived a controversial referral decision to keep South Africa in charge of the fourth and final Test against England in Johannesburg on Friday.
The tourists have made an official complaint after the opener was given not out on 15 when he appeared to edge a delivery from the recalled Ryan Sidebottom to wicketkeeper Matt Prior.
Captain Andrew Strauss referred the decision to video umpire Daryl Harper, but the Australian apparently rejected the appeal as he could not hear the snick -- he had the volume turned down on his television speaker, according to England coach Andy Flower.
"In a subsequent discussion with [match referee] Roshan Mahanama, he informed us Daryl simply didn't turn up the volume," Flower said.
"It is not the end of the world and it is a Test match, but it was at a crucial time. He is one of the most important wickets in their line-up."
Smith went on to make 105, his 20th Test century and second successive three-figure score, as the Proteas reached 215-2 on a second day shortened by rain and bad light.
That put the home side, who need to win to tie the four-match series 1-1, 35 runs ahead with eight wickets in hand after dismissing England for 180 on Thursday.
Resuming on 29-0, South Africa lost Ashwell Prince seven runs later for 19 as the out-of-form makeshift opener edged a ball from seamer Chris Broad to Graeme Swann.
Smith and Hashim Amla then followed up the 230 they put on in Cape Town with a second-wicket stand of 165 in 41 overs.
Left-arm quick bowler Sidebottom, celebrating his return to the side on his 32nd birthday in place of Graham Onions, finally had his reward when he had Smith caught at slip by Strauss. The left-hander hit 16 boundaries from 187 deliveries.
But England were unable to take advantage of the breakthrough as a thunderstorm saw the day reduced by 46.4 overs.
More than three hours later, Amla and Jacques Kallis came back to face 23 balls before bad light finally brought an end to play.
Amla was unbeaten on 73, having hit eight boundaries from 132 balls faced.
Ponting, who was dropped before he scored on Thursday, added 72 runs to his overnight 137 as he added 352 for the fourth wicket with Michael Clarke (166).
The home side declared at 519-8 and dominated the final session of the second day as Pakistan slumped to 94-4 -- still 226 runs from avoiding the follow-on.
The tourists lost captain Mohammad Yousuf and another key batsmen Umar Akmal to run-outs, with opener Salman Butt at fault both times as he stood his ground at the other end.
Butt now has a huge responsibility on his shoulders after ending the day unbeaten on 34 along with Shoaib Malik, Pakistan's only other remaining specialist batsman.