The AFL cancelled the game after two chartered light aircraft carrying Essendon players and coaches were forced to return to Melbourne after being unable to land in Wangaratta, which had been drenched by rain throughout the week. St Kilda took a bus to the ground on Friday.
Initially, the AFL said the points would be shared between the clubs, but a statement released on Sunday afternoon announced a revision of the decision.
"The AFL noted that extreme weather conditions meant that Essendon was unable to reach Wangaratta by air for the match. However, it also resolved that alternate travel arrangements were available to the club and therefore Essendon's inability to attend the match was ultimately within its control," the statement said.
St Kilda said on Sunday morning that it would not formally seek to be awarded the points, despite coach Scott Watters earlier saying his club deserved them.
AFL operations manager Adrian Anderson acknowledged the decision to abandon the match and award the points to the Saints was unusual.
"Essendon has informed the AFL they were assured by the airline operators that the aircraft could reach Wangaratta based on the weather forecast at the time of departure," Anderson said.
"Clearly flying conditions changed dramatically over the course of the flight and the repeated efforts by the pilots to land in the region were only thwarted by the shocking weather conditions and related safety considerations.
"Essendon has already indicated today (Sunday) that it will be looking at ways to directly thank the local community for their understanding and the AFL has also informed local authorities that we will make every effort to schedule a NAB Cup game in Wangaratta next year."
Anderson said the League would review pre-season arrangements to ensure a similar situation does not re-occur.
The two Wangaratta football clubs hosting the game hold no grudges.
Wangaratta Magpies president Paul Challman told Melbourne's SEN radio station: "We're not blaming anyone - we're blaming the weather.
"Look, if it was played on Friday (the weather) was perfect, and if it was played yesterday (Sunday) it was perfect. It was just bad luck it rained on Saturday."
Challman said the two local clubs had been guaranteed several AFL-level games over the next decade and would love to be allocated another NAB Cup game next year.
Essendon CEO Ian Robson said the Bombers would be keen to return next year.
"We'd be delighted.... I'm conscious of all of the hurt now that there's a financial hurt to the two (Wangaratta) footy clubs (and) the hurt of seeing kids sitting around on the boundary line …
"People were sitting out in the rain for hours.
"What St Kilda did (in playing an intra-club practice match) was a marvellous act of goodwill in the circumstances to put their boys out on the deck in the rain and the wet.
"I will sit down with the VCFL and the AFL. We'd be happy and delighted to put up our hand to go back there next year for the NAB Cup."
