The Frenchman secured a top five finish on the day as his Mini team-mate Nani Roma came through strongly to win the 392km stage between Fiambala and Copiapo.
But Peterhansel's lead over the Toyota of Giniel de Villiers is a full 50 minutes and 21 seconds, with Roma a further 40 minutes adrift.
De Villiers, despite admitting it had been a difficult day, said he had not given up hope of overhauling the Dakar veteran.
"We're trying," he said, "and it's not over yet."
Stage 12 results
1 Nani Roma (ESP) 3:36:34
2 Robby Gordon (USA) 3:40:52 +04:18
3 Giniel de Villiers (RSA) 3:40:59 +04:25
4 Stéphane Peterhansel (FRA) 3:42:37 +06:03
5 Orlando Terranova (ARG) 3:43:00 +06:26
6 Lucio Ezequiel Alvarez (ARG) 3:45:59 +09:25
7 Carlos Sousa (POR) 3:46:32 +09:58
8 Ronan Chabot (FRA) 3:46:52 +10:18
9 Leonid Novitskiy (RUS) 3:51:44 +15:10
10 Zhou Yong (CHN) 3:59:22 +22:48
Overall standings
1 Stéphane Peterhansel 32:50:02
2 Giniel de Villiers + 50:21
3 Nani Roma + 1:31:06
4 Leonid Novitskiy + 1:34:47
5 Orlando Terranova + 2:01:50
6 Carlos Sousa + 2:39:46
7 Ronan Chabot + 3:03:11
8 Pascal Thomasse + 4:14:26
9 Geoffrey Olholm + 4:29:11
10 Boris Garafulic + 4:32:00
