The Scottish Rugby Union (SRU) has opted not to appeal the £70,000 ($90,000/€80,000) fine issued by World Rugby for comments made by chief executive Mark Dodson at the World Cup in Japan.
Dodson was sanctioned for remarks made before Scotland's clash with the host nation, which was threatened by Typhoon Hagibis.
If the match had been cancelled the Scots would have exited the tournament without having the chance to play, and Dodson questioned World Rugby's "rigidity".
He hinted at legal action in case of an abandonment and said he would not allow Scotland to become "collateral damage".
An Independent Disputes Committee chaired by England's Christopher Quinlan ruled that the statements amounted to misconduct.
Scotland were also ordered to write a "meaningful" apology to World Rugby and World Cup organisers, and were formally reprimanded.
In the end the game did go ahead on October 13, with Japan winning 28-21 in Yokohama to send Scotland home.
The SRU had claimed they could respond to their punishment with arbitration.
However, World Rugby said today the case had been settled.
"World Rugby can confirm that the Scottish Rugby Union has expressed its regret and has confirmed it will not challenge World Rugby further on this matter," a statement said.
"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."
Typhoon Hagibis resulted in the loss of nearly 90 lives in Japan and forced the cancellation of three Rugby World Cup matches last month.
The fine will be donated to the Childfund Pass it Back programme, which is assisting the typhoon relief effort.
World Rugby claimed there had been "ample time" to solve the dispute without formal proceedings.
They made an offer which required the SRU to apologise for its conduct and make a donation to the typhoon disaster fund.
However, the SRU suggested alternative wording, including a mutual expression of regret, and no apology, World Rugby said.
A second charge relating to comments by SRU legal counsel Nick De Marco and an "SRU spokesperson" was dismissed.