World Rugby says the Scottish Rugby Union has "expressed its regret" over conduct at the World Cup and will not contest a £70,000 fine.
The penalty came after criticism of the threatened cancellation of Scotland's final pool game against Japan.
The match was in doubt because of the approaching Typhoon Hagibis, and SRU chief executive Mark Dodson complained of World Rugby's "rigidity".
Dodson hinted at legal action if the match did not go ahead.
An independent disputes committee later ruled he had "brought the game into disrepute" and imposed the fine.
A statement from World Rugby read: "[We] can confirm the Scottish Rugby Union has expressed its regret and has confirmed it will not challenge World Rugby further on this matter.
"The Scottish Rugby Union has agreed to pay a donation of £70,000 to World Rugby and the matter is now closed. There will be no further comment from either party."
Cancelling the final pool game against the host nation would have eliminated Scotland and, after two matches scheduled for the previous day had been called off, World Rugby said it would make a decision on the day of the match about whether it could go ahead in Yokohama.
The game was played, but Scotland lost 28-21 and failed to reach the knockout stage.
At the time of the independent disputes committee initial ruling, Scottish Rugby responded by saying: "We will now reflect on this outcome and further consider all our options, which may include arbitration."
'Bitterness remains amid nuance & subtlety' - analysis
BBC Scotland's chief sports writer Tom English
World Rugby was looking for a grovelling apology from the SRU and it hasn't got it. The SRU was going for a joint statement of regret with World Rugby and it hasn't got it either. This is a middle-ground solution. Neither body has got what it wanted but both can claim to be satisfied with the outcome.
As for the £70,000 sanction that World Rugby's independent disputes committee handed out in its lacerating judgement of last week, that money will be handed over by Murrayfield. Again, there are nuances that illustrate how hard-fought this battle was.
World Rugby's disputes committee has called it a fine. Scottish Rugby is calling it a donation. World Rugby's committee wanted the money to go directly to the Typhoon Hagibis disaster relief fund. The SRU is instead giving it directly to World Rugby, who will presumably pass it on to the disaster fund.
There's a subtlety here. Some might call it a pettiness, but it matters to the SRU. In the days leading up to Typhoon Hagibis - a horror that would kill 89 people - World Rugby accused the SRU of insensitivity in its campaign to get the Japan versus Scotland game played. In its verdict last week the disputes committee firmly backed that view.
The SRU was incensed at that interpretation and felt that if it gave the £70,000 to the disaster fund then it could be interpreted as accepting it had been guilty of insensitivity towards the victims of Hagibis and was now trying to make amends. It wants the £70,000 to go to the disaster fund, but it is also thinking of what that might look like.
This might bring this business to a close but the bitterness remains. On both sides.