Cheteshwar Pujara took his score on to 153 and Virat Kohli was dismissed four short of a hundred prior to India being bowled out for 421 in their second innings.
The tourists' effort ensured South Africa would need to pull off a record fourth-innings chase in order to clinch a shock win, or bat for more than four sessions to avoid defeat.
Yet Petersen did his best to keep his side's hopes alive, sharing an opening stand of 108 with captain Graeme Smith (44) before reaching stumps unbeaten with 76 of South Africa's 2-138.
Smith's men will begin the final day requiring a further 320 to pull off an unlikely triumph, with Faf du Plessis (10 not out) also at the crease.
India resumed on 2-284 in their second innings, having amassed a healthy lead on day three.
The partnership between Pujara and Kohli, worth 191 overnight, reached 222 before the former was eventually dismissed, edging a cut behind off Jacques Kallis (3-68).
Rohit Sharma (6) also fell to Kallis before Kohli, needing one boundary to complete his second hundred in the match, feathered a catch through to wicketkeeper AB de Villiers off JP Duminy.
South Africa made regular inroads thereafter, although MS Dhoni and Zaheer Khan each contributed 29 to enhance India's position.
Facing a daunting task, South Africa made solid progress either side of tea through Petersen and Smith.
The pair batted together for more than 30 overs before Smith, seeking a quick single to mid-on, was run out by Ajinkya Rahane's direct hit.
Hashim Amla added only four before being deceived and bowled by a delivery from Mohammed Shami (1-30) that kept low.
Yet Petersen held firm alongside Du Plessis to deny India further success before the close.