Adnan Cirak's injury-time strike kept Stockport's hopes of Blue Square Bet Premier survival alive and prevented Gateshead from securing safety.
The visitors had large periods of possession and made chances for Cirak and Daniel Whitehead.
But Gateshead took a second-half lead when James Curtis rolled the ball across for Josh Gillies to finish.
However, the home side were denied the chance to celebrate avoiding the drop as Cirak netted a loose ball late on.
Stockport still occupy the final relegation spot going into Saturday's final day of the season and are two points adrift of Tamworth and Gateshead above them.
Lincoln City, a point further clear, could also still mathematically go down.