The Spaniard endured a difficult start to the event, with a breakdown 10 kilometres into stage one costing him two hours and severely hampering the Mini driver's chances of defending his crown.
Roma has refused to lie down, though, and picked up podium finishes on stages four and six prior to Tuesday's triumph on the ninth leg.
The 42-year-old completed the 450km route from Iquique to Calama in four hours and 41.56 seconds, almost five minutes ahead of second-placed Nasser Al-Attiyah who posted a time of 4:48.23.
"It was quite a hard stage," said Roma. "At the beginning there were some dunes and, after some hard track and a lot of fesh-fesh, some navigation.
"It was not easy, but it was quite good and I'm happy to be here in Calama for the last stage in Chile.
"Tomorrow we go into Argentina again and it's four days to the finish. So yes, I'm quite happy now."
Despite being convincingly beaten by Roma, team-mate Al-Attiyah took a huge leap towards securing the overall win by stretching his advantage at the head of the field to almost 24 minutes.
Toyota's Giniel de Villiers - eight and a half minutes down heading into stage nine - came home fourth on Tuesday, 15 and a half minutes adrift of Al-Attiyah.
Third-placed Yazeed Al-Rajhi (Toyota) lost yet more ground and now sits almost 40 minutes off the lead in fourth place, while Mini's Vladimir Vasilyev finished third to achieve his second podium of the event.