The association said they will purchase the 52,000-capacity stadium from League Two side Queen's Park FC for five million pounds, with Scottish businessman Willie Haughey pledging to pay half the amount.
"Today's announcement has been the conclusion of a four-year process to review our national stadium beyond 2020," Scottish FA President Alan McRae said.
"It was a hugely difficult decision and I would like to place on record our thanks to Scottish Rugby for their professionalism throughout the process.
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"This decision is about what was best for Scottish football and our members. It's about the future of football in Scotland."
The seven-member Scottish FA board, which delayed a decision on the venue late in August, eventually chose Hampden which has hosted the national team's matches since 1906 as well as major cup finals involving Scottish clubs.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Christian Radnedge)
