Atherton, 28, has won all seven races this season and 13 in a row, a run stretching back to 2015.
The world champion had already sealed the 2016 World Cup crown in Canada last month but won in Andorra on Saturday to end the World Cup season unbeaten.
She has now won five overall World Cup titles in downhill.
Wales' Manon Carpenter completed a British one-two in the overall standings, finishing 560 points behind Atherton.
Trek Factory Racing's Atherton won the final race by 6.5 seconds ahead of Australian Tracey Hannah and Myriam Nicole of France.
In the men's event, Britain's Danny Hart won his third consecutive World Cup race but finished second in the overall standings behind American Aaron Gwin.

The Mourne County were 4-1 outsiders for their semi-final against Monaghan but clinched a 1-14 to 0-15 victory.
"I'm confident if we go there and express ourselves and play hard, we have a realistic chance of becoming Ulster champions," says Burns.
"But we know that it's going to be a huge task."
1991 and 1994 All-Ireland medallist Burns endured a torrid start to his Down managerial stint as his side lost 11 straight competitive games before a remarkable escape act earlier this year saw them avoid a second successive league relegation as they remained in Division Two.
"When I took over the job, I knew there were going to be tough times ahead. I had prepared for that but at times there was quite a bit of undue criticism of the team," adds the Down boss.
"Whenever I took the job, I lost maybe eight or 10 players and they were the most experienced players in the panel.
"So you are starting from scratch as such. You are having to start and build a panel and you are bringing in young and inexperienced players who might have played at minor and under-21 level.
"There is a massive step up from under-21 to having to play at senior level. But we worked away, we kept our heads down, we introduced quite a few players and the ball is starting to roll in the right direction for us."
Burns believes the concluding league draw in Cork which kept Down in Division Two as Derry and Fermanagh suffered the drop was a key moment in his team's development.
"We knew we were going to have to get something when we were down there and it had been a long time since Down had got anything in Cork.
"We had a tough second half with them but we battled it out and the result kept us in Division Two and gave us a platform to build on in the lead-in to the championship."
Despite avoiding the drop to join Armagh in Division Three, Down still went into the Ulster derby against the Orchard County on 4 June as underdogs but the Mournemen produced a composed second-half display to earn a deserved 0-15 to 2-7 victory.
"We knew if we performed on the day that we had a massive chance of beating Armagh. That result gave us a great boost and then we had another great win against Monaghan."
Burns' matter of fact description of belies the emotion he showed at the final whistle of the provincial semi-final in the Athletic Grounds as he emotionally embraced the Down county secretary Sean Og McAteer.
"I think there are a couple of of pictures of me hugging him. It was just great to give the players an opportunity to play in an Ulster Final. The players had taken the brunt of the criticism when we struggled after I took on the job."
As for Sunday's final, Burns knows full well that his side be even bigger underdogs than in their two most recent games.
"Tyrone are laden with a lot of experience and a lot of talent. They play in Division One and had a good league campaign this year.
"They have played in Croke Park for the last four or five years so yes it's going to be very difficult for us.
"But we have a lot of self-belief and inner strength which we are going to have to dig into and use to battle hard if we are going to get a result."
Britain's Rachel Atherton completed the first "perfect season" in UCI Downhill Mountain Bike World Cup history with victory in the season's final race.
[NEXT_CONCEPT]
Down manager Eamonn Burns believes his side are capable of causing another shock by beating holders Tyrone in Sunday's Ulster Football Final.