Kluwe had accused the Vikings of cutting him in May of 2013 because of his vocal support of marriage equality and gay rights.
Terms of the settlement were not disclosed.
As part of the settlement, Minnesota have agreed to provide financial support for human rights causes. The team will also continue to enhance its sensitivity training policy and will help raise awareness in professional sports about LGBT issues.
Kluwe claimed in a January that special teams coordinator Mike Priefer made an anti-gay comment at a team gathering. The National Football League club conducted an internal probe and suspended Priefer for three games in July.
Kluwe averaged 44.4 yards per punt over his eight seasons with Minnesota.