The decision means the last 38 kilometres don't count and the stage ends at checkpoint #53, at the 389km mark.
There was confusion at the end of the stage for riders such as Price and Xavier De Soultrait as the duo got lost, which cost them a significant amount of time.
As Price explained, his problem stemmed from GPS showing a checkpoint in a wrong position.
"Right at the end there is a WPC [Control Waypoint, to which no directions are supplied by GPS] that was... it’s in the roadbook but not in the correct place," Price said. "So I spent a lot of time trying to find this and lost a lot of time there.
"Finally found it. But the WPC is not meant to have an open arrow [on the GPS]. And the arrow opened for it, and it was sitting basically on the top of a rocky mountain ridge. So I thought there might have been a road on the back side of it.
"So I tried to climb up and over and get to the other side and yeah, just a bit of chaos and carnage."
Ricky Brabec still won the stage from Jose Ignacio Cornejo but by only 5m56s instead of his original 9m39s gap.
Joan Barreda dropped from third to sixth but Kevin Benavides still completed an all-Honda top three on the day.
Meanwhile, Walkner and Price have moved up to fourth and fifth, as more than half of their original deficit was erased.
In the overall order, Brabec leads Kevin Benavides by 4m43s, with Walkner up to third followed by two more Hondas in Barreda and Cornejo.
Amended standings after Stage 3 (Bikes, top 10):
|5||Jose Ignacio Cornejo||Honda||11m19s|
|10||Xavier de Soultrait||Yamaha||19m55s|