Petrucci continued his strong start to his rally-raid career with a provisional second place on Thursday's stage, a 346km loop around Riyadh, finishing four minutes, 14 seconds behind fellow KTM man Price.
However, it was subsequently announced that Price had been handed a six-minute penalty for speeding, handing Petrucci his first Dakar stage win in just his fifth attempt.
With Price dropping to sixth on the stage after his penalty, Yamaha's Ross Branch moves up to second, followed by Honda pair Pablo Quintanilla and Jose Ignacio Cornejo, and another impressive KTM rookie, American Mason Klein.
Petrucci's stage win followed a day on from a strong ride to third place on Wednesday's fourth stage of the rally, albeit he was also awarded a 10-minute penalty for speeding that dropped him to 15th.
However, the Italian's hopes of figuring strongly in the fight for overall honours were effectively ruined on Monday, when he suffered a problem on the second stage that he couldn't fix without assistance.
Under new Dakar rules, Petrucci was permitted to rejoin the rally with heavy penalties that had left him 130th overall as of Wednesday night.
A new overall bikes classification was issued after the stage was cut short due to a lack of medical aircraft, but the lead contenders were not affected.
GasGas rider Sam Sunderland is still 2m29s clear of KTM's Matthias Walkner at the top of the table, with Adrien van Beveren third for Yamaha.
However, fifth-placed Skyler Howes (Husqvarna) has been forced to withdraw from the rally despite finishing the stage, as he was injured in a heavy crash.
Honda's Joan Barreda, who has moved up to 10th overall following Howes' retirement, likewise suffered a fall and hurt his shoulder, and will make a decision on Friday morning whether to continue.
Revised standings after Stage 5:
| Pos. | # | Name | Bike | Time | Gap | Penalty |
|---|---|---|---|---|---|---|
| 1 | 3 | Sam Sunderland | KTM | 19:01:50 | 00:00:00 | |
| 2 | 52 | Matthias Walkner | KTM | 19:04:19 | +00:02:29 | 00:00:00 |
| 3 | 42 | Adrien van Beveren | YAMAHA | 19:07:49 | +00:05:59 | 00:00:00 |
| 4 | 4 | Daniel Sanders | KTM | 19:09:51 | +00:08:01 | 00:00:00 |
| 5 | 15 | Lorenzo Santolino | SHERCO FACTORY | 19:17:17 | +00:15:27 | 00:00:00 |
| 6 | 7 | Pablo Quintanilla | HONDA | 19:18:45 | +00:16:55 | 00:00:00 |
| 7 | 16 | Ross Branch | YAMAHA | 19:20:05 | +00:18:15 | 00:00:00 |
| 8 | 1 | Kevin Benavides | KTM | 19:23:41 | +00:21:51 | 00:00:00 |
| 9 | 142 | Stefan Svitko | KTM | 19:24:40 | +00:22:50 | 00:00:00 |
| 10 | 88 | Joan Barreda | HONDA | 19:24:48 | +00:22:58 | 00:01:00 |
