Tobias Werner put the home side in front after just five minutes at the SGL-Arena, but Netherlands striker Huntelaar levelled 12 minutes before half-time and then struck again four minutes after the break to seal the points less than a week after scoring a half-trick against Hoffenheim.
The victory moved the Gelsenkirchen side three points clear of Bayer Leverkusen in third place ahead of Leverkusen's trip to runaway leaders Bayern Munich on Saturday and Huntelaar was relieved to grind out the victory despite admitting the visitors were not at their best.
He is quoted as saying on the official Bundesliga website: "It was important we equalised just before half-time.
"We didn't start well - we made far too many individual mistakes and just couldn't get into the game in the first half, but we still fought to try to win the game and, thankfully, we managed to get the three points."
Schalke midfielder Kevin-Prince Boateng praised Huntelaar after he followed up his treble last weekend by helping himself to a brace.
The Ghana international said: "We were asleep for the entire first half, but 'the Hunter' was in the right place in the right time to score the two goals.
"We knew it would be very difficult for us today. Augsburg are a very good side - it's no coincidence they're near the top of the league, but we're happy to win."
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