The South Korean carmaker, which with affiliate Kia Motors makes up the world's fifth largest auto group, signed up in 2010 to become FIFA's official automotive partner until 2022.
Hyundai-Kia is a presenting sponsor for the 2018 World Cup in Russia, along with the likes of Adidas, Coca-Cola, Visa, Budweiser and McDonald's.
Hyundai, which had voiced deep concern following the arrest of seven FIFA officials in Switzerland for bribery last week, said Blatter's decision to step down would allow comprehensive reform of the way FIFA is run.
"We remain committed to supporting the fan passion of football around the world," it added.
The Hyundai response was largely in line with similar statements issued by Coca-Cola, Visa and Adidas.
Major sponsors pay an estimated $30 million a year each to be official partners of FIFA, giving them the right to promote their products at football games and other events around the world.
