American McCarthy was penalised by two shots under Rule 10.2b(4), which does not allow caddies to stand behind players as they line up their shot.
But golf's ruling bodies, The Royal & Ancient and the United States Golf Association, have said the penalty should not have been applied and the Tour has reversed the initial decision made during the second round.
In a joint statement the R&A and USGA said: "Following an ongoing dialogue with players and in co-operation with the PGA Tour rules team, The R&A and the USGA revisited the penalty assessed to Denny McCarthy during round two of the Waste Management Open.
"After an additional review of available video (on Saturday) morning, it was determined that the penalty would not apply in this instance nor in a similar instance involving Justin Thomas.
"In each of these cases, when the caddie was standing behind the player, the player had not yet begun taking the stance for the stroke, nor could useful guidance on aiming be given because the player was still in the process of determining how to play the stroke.
"The same would be true for any similar situation that might occur."
The R&A and the USGA said clarity on how to appropriately apply the rule was needed and that they "will provide the necessary clarifications in the coming days".
During last week's Omega Dubai Desert Classic, Li Haotong was penalised two shots because his caddie was on a direct line behind the ball when he began to take his stance on the green.
European Tour chief executive Keith Pelley expressed his concern at the "grossly unfair" penalty, which meant defending champion Li dropped from a tie for third to a tie for 12th, costing him more than 80,000 euros (£70,000).
But after reviewing Li's case The R&A released a statement last Sunday saying the referees had correctly applied a two-shot penalty in that instance.
