Leipzig moved back to Champions League place following a massive victory whilst Schalke slide down the table after an error-strewn display.
RB Leipzig star Werner, who has been heavily linked with a move to Liverpool, hit three in an 8-0 win over Mainz in November and repeated the trick in a 5-0 success at Opel Arena this weekend.
Timo Werner became the first Bundesliga player to score two hat-tricks against the same opponent in a single season in 21 years with his treble against Mainz on Sunday.
The last player to register hat-tricks in two games against one opponent in the same Bundesliga season was Bayer Leverkusen’s Ulf Kirsten against Borussia Monchengladbach in 1998-99.
Germany international Werner’s tally for the 2019-20 campaign now stands at 30 in all competitions – the best single-season return of his career.
Meanwhile, Schalke are now winless in nine games, and have scored only twice in that run following a bitter 3-0 defeat to Augsburg on Sunday.