The 35-year-old replaces Rob Elliot, who left earlier this month to take over at Crawley Town.
Magnay, a former player for the Heed, was a coach under Mike Williamson before his departure to Milton Keynes.
He followed the manager to Carlisle United but now feels the time is right to step up and be a number one.
Magnay is joined by Liam Bridcutt who becomes first team coach at the International Stadium.
"We are delighted to be able to confirm the appointments of Carl and Liam," said chairman, Neil Pinkerton.
"It was hugely important to the Board of Directors that the necessary time be taken to bring the right people to Gateshead Football Club, and we appreciate our supporters' patience over recent weeks.
"We are fully confident that Carl is the right person to continue the club's progression - just as he has done in his previous spells as a player and a coach and we look forward to seeing he and Liam get to work this week."