The Argentine came in behind stage winner Sarel Van Biljon and Sebastian Husseini on the day but did enough to equal the record held by his older brother Alejandro - of two overall wins - following his last success in 2010.
Patronelli had led the overall standings from stage two and won it with 1h 50′35″ to spare over Chile's Ignacio Casale and 3h 16′40″ over Poland's Rafał Sonik.
"It was spectacular," Patronelli said. "This Dakar was like a dream come true for me. Everything went smoothly from the first day in Peru to the last in Chile.
"I'm surprised at how the stages went. This victory means a lot to me. My brother won last year, but I ran into trouble. I was here to get my own back on myself.
"Ale [Alejandro] and I don't compete with each other. I wanted to prove myself that I could win again. It was a perfect Dakar from the beginning to the end. It's the first time that everything's played out so well."
On the final special, Van Biljon won his third stage in 2013, although he still finished 21st on the overall standings.
Stage 14 result
1. Van Biljon (ZAF/E-ATV) 01:54:05
2. Husseini (ARE/Honda) 01:54:42
3. Patronelli (ARG/Yamaha) 01:55:23
4. Laskawiec (POL/Yamaha) 01:55:24
5. Casale (CHL/Yamaha) 01:55:34
6. Boneto (ARG/Honda) 01:55:38
7. Sonik (POL/Yamaha) 01:57:29
8. Smith (AUS/Honda) 01:57:40
9. Maffei (ARG/Yamaha) 01:58:38
10. Duverney-Pret (FRA/Yamaha) 02:00:08
1. Patronelli (ARG/Yamaha) 49:42:42
2. Casale (CHL/Yamaha) 51:33:17
3. Sonik (POL/Yamaha) 52:59:31
4. Bonetto (ARG/Honda) 53:22:52
5. Palma (CHL/Can-Am) 54:18:39
6. Husseini (UAE/Honda) 55:22:45
7. Smith (AUS/Honda) 55:28:51
8. Flores Seminario (PER/Yamaha) 55:52:09
9. Clavigliasso (ARG/Can-Am) 56:02:23
10. Gagliardi (ARG/Yamaha) 56:12:18