Despite only finishing fourth on Saturday’s 157km run from La Serena to Valparaiso in Chile, Roma was crowned champion after rival Peterhansel deliberately slowed, finishing 13th on the stage and second overall.
South Africa’s Giniel de Villiers took the stage victory with Mini pair Krzysztof Holowczyc and Vladimir Vasilyev finishing second and third respectively.
Roma’s triumph capped a confusing rally which saw his X-Raid Mini team receive widespread criticism for enforcing team orders on Thursday's 11th stage to protect a podium sweep.
“I don't know if this was the most stressful thing I'd ever done, but it was very tough,” said Roma.
“The second week, with difficult, long stages, wasn't easy. I'm going to revel in this.”
Peterhansel added: “Let's look on the bright side of things. The car didn't miss a beat, it took anything we threw at it, like usual, and we had lots of fun driving.
“But I'm frustrated with the final result. The third thing I want to say is that Nani's my friend, and I'm pleased to see him happy because it's been his dream for ten years, since he shifted to a car.”
Cars – stage 13 results
1 Giniel de Villiers (RSA) 1:57:07
2 Krzystof Holowczyc (POL) 1:57:30 +23
3 Vladimir Vasilyev (RUS) 1:57:48 +41
4 Nani Roma (ESP) 1:58:47 +01:40
5 Orlando Terranova (ARG) 1:59:00 +01:53
6 Christian Lavieille (FRA) 2:00:04 +02:57
7 Federico Villagra (ARG) 2:00:16 +03:09
8 Martin Kaczmarski (POL) 2:01:52 +04:45
9 Nasser Al-Attiyah (QAT) 2:01:58 +04:51
10 Boris Garafulic (CHI) 2:04:06 +06:59
1 Nani Roma 50:44:58
2 Stéphane Peterhansel + 5:38
3 Nasser Al-Attiyah + 56:52
4 Giniel de Villiers + 1:19:07
5 Orlando Terranova + 1:27:44
6 Krzystof Holowczyc + 3:55:42
7 Marek Dabrowski + 5:34:25
8 Christian Lavieille + 5:35:50
9 Martin Kaczmarski + 6:58:12
10 Vladimir Vasilyev + 6:59:34