X-raid Mini's Stephane Peterhansel had been credited with the fastest time on the stage initially, while Sainz - the leader after the first day - had lost over 20 minutes and fallen to 11th overall.
Following an overnight investigation by rally organisers, the 21m26s lost by Sainz as he searched for a waypoint, has now been given back to the Red Bull Buggy driver.
The Spaniard's problem was caused by the satellites used by the rally organisers, rather than his own in-car GPS unit.
"It was really strange out on the stage because of the problems we had with navigation," said the two-time World Rally champion.
"There was a waypoint on the stage that we passed three or four times before it would let us continue on the stage.
"We were going up and down and round and round because we knew we were in the right place.
"Eventually we decided to leave because we just couldn't find this waypoint. This was a risky move because if you do not pass all the waypoints on the stage it can cost you a time penalty.
"Then after we travelled 3km away we got the waypoint confirmation. The whole thing was very strange."
Revised positions after stage two:
Pos Driver Team/Car Time/Gap
1. Carlos Sainz Red Bull Buggy 2h55m15s
2. Stephane Peterhansel X-raid Mini + 5m05s
3. Giniel de Villiers Imperial Toyota + 7m43s
4. Ronan Chabot SMG Buggy + 8m51s
5. Orlando Terranova X-raid BMW + 11m31s
6. Leonid Novitskiy X-raid Mini + 14m38s
7. Lucio Alvarez Overdrive Toyota + 17m32s
8. Krzysztof Holowczyc X-raid Mini + 19m05s
9. Carlos Sousa Great Wall + 20m53s
10. Bernard Errandonea SMG Buggy + 22m20s
Leading stage two times:
1. Carlos Sainz Red Bull Buggy 2h32m15s
2. Stephane Peterhansel X-raid Mini + 3m32s
3. Giniel de Villiers Imperial Toyota + 5m58s
4. Ronan Chabot SMG Buggy + 8m15s
5. Orlando Terranova X-raid BMW + 8m49s
6. Leonid Novitskiy X-raid Mini + 12m56s
7. Nasser Al-Attiyah Red Bull Buggy + 15m00s
8. Lucio Alvarez Overdrive Toyota + 17m08s
9. Krzysztof Holowczyc X-raid Mini + 17m23s
10. Carlos Sousa Great Wall + 17m56s