The Netherlands international came into the clash on 98 goals for the Gelsenkirchen club but needed just over an hour to hit his 100th Schalke goal and ease them to consecutive league wins.
Roberto Di Matteo's side were humbled 5-0 by Chelsea in the UEFA Champions League on Tuesday but recovered well on their return to domestic action, assuming the lead through Huntelaar's flick nine minutes in.
The former Real Madrid man then moved to 100 goals for Schalke before the half-hour mark, with Shinji Okazaki's strike before the interval the only negative for Di Matteo.
However, Tranquillo Barnetta restored the two-goal lead early in the second half before Huntelaar completed his hat-trick - having previously failed to score for Schalke since October.
Bayer Leverkusen also enjoyed a dominant home win - Josip Drmic and Karim Bellarabi each scoring twice in a 5-1 victory over Cologne.
Matthias Lehmann had given the visitors a surprise lead at the BayArena before Bellarabi levelled matters before the break.
Hakan Calhanoglu put Roger Schmidt's side in front after the hour before Drmic completed a quickfire brace, with Bellarabi rounding off the scoring.
Hamburg's inconsistency was again on show at the SGL Arena as they threw away a one-goal lead in their 3-1 defeat to Augsburg.
Second-half goals from Halil Altintop, Raul Bobadilla and Paul Verhaegh cancelled out Rafael van der Vaart's opener as Hamburg lost for the third time in five Bundesliga outings.
Champions Bayern Munich maintained their unbeaten league record this term against Hertha Berlin - Arjen Robben scoring the decisive goal in the capital - while Werder Bremen ran out 4-0 winners against Paderborn.
Zlatko Junuzovic, Davie Selke, Fin Bartels and Levent Aycicek were all on target for Viktor Skripnik's men while Hoffenheim and Hannover played out a seven-goal thriller in the day's final game.
Despite letting a 2-0 lead slip, Hoffenheim recovered to eventually win through 4-3 and end a run of three consecutive Bundesliga games without a win.
