Going into the race, Makarainen trailed Tora Berger by five points with the Norwegian looking to take the title in front of her home fans and end her career on a high.
However the pair were not even competing at the front of the field, with Slovakia's Anastasiya Kuzmina instead leading the charge.
Kuzmina had won the pursuit race on Saturday and took her second successive victory by 3.8seconds, crossing the line in a time of 39:44.8minutes.
Second went to Teja Gregorin of Slovenia with Marie Dorin Habert from France in third while Darya Domracheva secured the mass start title with fourth.
But with Makarainen crossing the line in seventh it saw her move onto 860 points, enough for her to take her second biathlon title by four points ahead of Berger, who finished in 14th.
Meanwhile the men's 12.5km pursuit saw Austria's Simon Eder take his first victory of the season - and first in five years - although it was Martin Fourcade who took both the pursuit and overall title.
Double gold medallist in Sochi, Fourcade had already wrapped up the overall title and came in fifth to take the pursuit title ahead of Eder.
Shooting clean, Eder secured victory in 32:23.40mins ahead of Russia's Alexander Loginov and Sweden's Bjorn Ferry.
- Sports & Recreation
- Tora Berger
- Anastasiya Kuzmina
- Marie Dorin Habert
- Darya Domracheva