Argentina's Benavides went into the 14th and final stage of the Saudi Arabian event 12 seconds behind Price, but won the 136km test stage by 55 seconds from his rival to clinch a second title to add to the one he won for Honda in 2021.
Husqvarna's Skyler Howes, who had led the contest heading into the rest day, finished third, five minutes and four seconds behind.
Benavides first took the overall lead following Wednesday's Stage 10, but lost time navigating as the first rider to take to the stage the next day, allowing Howes to regain the advantage.
Price then moved to the top of the provisional standings for the first time in the rally on Friday's Stage 12, which marked the second half of the 'marathon' stage in which crews are not allowed any external assistance.
The Australian, who was aiming for a third Dakar crown, kept the lead by the most slender of margins heading into Sunday's final showdown as Benavides took his first stage win of the rally in Stage 13.
However, Price dropped some 1m49s to Benavides in a muddy opening part of the final stage and couldn't make up the deficit over the remaining kilometres, ending up a provisional third on the day behind both Benavides and GasGas rider Daniel Sanders.
Howes was only 1m31s behind Benavides into the final stage but dropped 3m45s to the eventual winner, albeit easily keeping hold of third overall.
Honda duo Pablo Quintanilla and Adrien van Beveren, the latter in his first appearance for the marque, completed the top five, while Luciano Benavides (Husqvarna) was sixth overall despite ending up with the most stage wins of anyone with three.
Sanders was handed a three-minute penalty on the final stage but this didn't affect his overall finishing position of seventh, while Honda's Jose Ignacio Cornejo was the final rider to finish within an hour of the leader.
As with the first week of the rally, the second week saw a number of high-profile names drop out of the event.
Chief among these was Joan Barreda, who reached the landmark of 30 career stage wins on his privately-entered Honda on Stage 4 but crashed out on Stage 9 immediately following the rest day with a fractured L2 vertebra.
On the same day, American KTM privateer Mason Klein, who had sat second only to Howes at the midpoint of the event, suffered two crashes, and while he was initially able to continue he finally withdrew ahead of the penultimate stage.
Another KTM rider, one-time Dakar winner Matthias Walkner, crashed on the penultimate stage and suffered lower back trauma that required him to be airlifted to hospital.
Fellow event winners Sam Sunderland (GasGas) and Ricky Brabec (Honda) were the among the casualties of the opening week.
Provisional standings after Stage 14:
| Pos. | Rider | Bike | Time | Penalties |
| 1 |
 Kevin Benavides |
KTM | 44h27'20 | 3'00 |
| 2 |
 Toby Price |
KTM | +00'43 | 1'00 |
| 3 |
 Skyler Howes |
Husqvarna | +05'04 | 1'00 |
| 4 |
 Pablo Quintanilla |
Honda | +19'02 | 2'00 |
| 5 |
 Adrien van Beveren |
Honda | +20'30 | |
| 6 |
Luciano Benavides |
Husqvarna | +22'42 | 1'00 |
| 7 |
Daniel Sanders |
GasGas | +25'57 | 7'00 |
| 8 |
 Jose Ignacio Cornejo |
Honda | +51'21 | |
| 9 |
 Lorenzo Santolino |
Sherco | +1h17'53 | 15'00 |
| 10 |
Franco Caimi |
Hero | +1h38'04 | 1'00 |
