Secure America's Future Elections Act or the SAFE Act This bill directs the National Protection and Programs Directorate of the Department of Homeland Security to designate the infrastructure used to administer elections as critical infrastructure. The bill amends the Help America Vote Act of 2002 with respect to: funding for states to upgrade the security of the information technology and cybersecurity elements of voting systems, voter registration lists, and voter registration processes; voting systems and cybersecurity standards; paper ballot and manual counting requirements; accessibility to voting systems and ballot verification for individuals with disabilities; durability and readability requirements for ballots; and mandatory manual audits of results of elections. The National Science Foundation shall make grants to study, test, and develop accessible paper ballot voting mechanisms and best practices to enhance the accessibility of paper ballot voting for voters with disabilities, voters whose primary language is not English, and voters with difficulties in literacy. The National Institute for Standards and Technology shall establish guidance for states that wish to establish alternative audit mechanisms. The Election Assistance Commission is made permanent.