The talented 20-year-old, who joined the club from VfB Stuttgart for a reported 10 million euros ($10.59 million) this season, took his tally to seven goals in the current campaign, as unbeaten Leipzig moved on to 30 points from 12 games.
Second-placed champions Bayern Munich host Bayer Leverkusen on Saturday, having lost their last two matches in all competitions.
Leipzig’s Naby Keita fired the opener from 18 metres after two minutes but Freiburg levelled in the 15th with Florian Niederlechner’s well-timed header from Pascal Stenzel’s cross.
Werner then took over, charging through to round goalkeeper Alexander Schwolow in the 21st minute and then rounding off a quick break with another goal 14 minutes later.
Marcel Sabitzer, who had earlier hit the post, made amends in the 79th by rifling home a low shot for Leipzig’s 10th goal in their last three matches.
($1 = 0.9441 euros)
(Reporting by Karolos Grohmann; Editing by Ken Ferris)
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