Oestberg came into the weekend of the World Cup Final in a commanding position after a strong performance in the Mass Start.
She was never able to truly trouble Nilsson but she did more than enough for a podium finish that saw her win the overall title, the first of her career.
Nilsson wins Pursuit as Oestberg takes overall title
Oestberg said afterwards: "It's hard to describe. I never could have dreamt of fighting for this jersey
"This year I managed to fight for it and the last few races have been tough physically and mentally during the fight with Natalia Nepryaeva and today when I managed to finish on the podium in the tour and can say I'm the winner of the overall World Cup is an unbelievable feeling."
World Cup champion Oestberg - It's an 'unbelievable' feeling
Nilsson finishes the season as the Sprint champion and after a terrific weekend in Canada she finishes as the World Cup final champion having won all three events.
Her performance caps off a brilliant end to the season for Sweden, with the country having seven of the top 15 finishers in the Pursuit.
Nilsson said: "I expected them to catch with me quite fast but when they didn't I thought 'okay let's keep going at my speed'.
Nilsson delighted to be able to enjoy final stages of race
"I was able to enjoy the end of the race and it's not so often I can do that!'
Therese Johaug, the overall Distance champion, pushed hard to catch Nilsson but was unable to keep up.