Borussia Dortmund can go top of the German league table with a win at Bayern Munich on Saturday night, but prior to the showdown, Leipzig took their chance to climb in the capital, where the Berlin Wall fell on November 9, 1989.
A replica of the Wall, which divided Germany's capital from 1961 until November 9, 1989, separated Hertha and Leipzig before being knocked down prior to kick-off as midfielder Maximilian Mittelstaedt gave the hosts a first-half lead in Berlin.
It lead lasted just six minutes as Hertha's Dutch defender Karim Rekik gave away a penalty with a handball, which Werner converted having hit a hat-trick in last weekend's 8-0 thrashing of Mainz.
Marcel Sabitzer added Leipzig's second on the stroke of half-time after the Austrian's first-time strike deflected off Rekik and wrong-footed Hertha's goalkeeper Rune Jarstein.
Midfielder Kevin Kampl added a late third with a superb left-footed strike from the edge of the area before Werner grabbed his second for his 11th league goals in as many games.
Hertha striker Davie Selke then added a late second against his former club.
The victory leaves Leipzig just a point behind leaders Borussia Moenchengladbach, who are home to Werder Bremen on Sunday.
Schalke blew the chance to go third, and level with Leipzig on 21 points, after conceding a late equaliser in their 3-3 draw at home to Fortuna Duesseldorf, which left the Royal Blues fifth.
Duesseldorf striker Rouwen Hennings completed his hat-trick five minutes from time as Fortuna picked up only their third league win this season.
Schalke squandered the lead three times after Daniel Caligiuri hit a superb first-half strike, then Turkey defender Ozan Kabak and Germany midfielder Suat Serdar scored second-half goals in Gelsenkirchen.
FC Union Berlin are up to 11th after their third straight win as Sebastian Anderson scored twice in their 3-2 victory at Mainz.
After Austrian defender Karim Onisiwo netted late on for Mainz, captain and right-back Daniel Brosinski, who conceded a first-half own goal, gave the hosts brief hope by scoring on a counter-attack to make it 3-2 on 90 minutes.
Augsburg climbed out of the bottom three with a 1-0 win at last-placed side Paderborn as defender Philipp Max, part of the Germany team which won men's football silver at the 2016 Olympics, scored their winner.