James Norwood rifled Latics ahead on the half-hour mark, giving keeper Archie Mair little chance with his strike.
However, fifth-placed Gateshead were thrown a lifeline when Stephen Wearne was on target in the 50th minute.
And the comeback was completed when Louis Storey stabbed home a follow-up 10 minutes later.
Micky Mellon's Latics, who dropped to 11th place in the table, are in action on Boxing Day when they travel to Hartlepool United.
