A 90th-minute penalty, converted by home striker Sebastian Polter, sealed the hosts' third league win this season on an emotional night at Union's sold-out Alten Foersterei stadium.
However, the referee had to march both teams off for six minutes at the start of the second-half after fireworks launched from the terraces landed on the pitch.
After the final whistle, a group of Union 'Ultras' — masked hardcore fans — invaded the pitch seemingly intent on confronting their Hertha rivals, before Union players persuaded them to return to the stands.
“It's a city derby and there was a lot of emotion,” said match-winner Polter.
“We, as players, wanted to make sure the (image of the) club wasn't harmed and we had a responsibility to prevent our fans from doing anything stupid.”
Nevertheless, hosts Union now enjoy bragging rights after an historic night for football in Germany's capital.
“To put it simply, it's the most important game of the season, definitely, more important than the (Bundesliga) championship, I would say,” Union fan Kenny Schwarz told AFP outside the stadium.
Next Saturday will mark 30 years since the Berlin Wall came down. Hertha had originally wanted to host the derby on the anniversary, an idea Union rejected.
'Not a friendship'
“I'm only 22,” laughed Schwarz. “I got all the coverage — that Hertha wanted to play on November 9 — but that doesn't mean much today.”
Just 26 kilometres (16 miles) separates Berlin's top clubs, but the Iron Curtain that divided communist East Germany from capitalist West Germany from 1961 kept the two clubs at a much greater distance until the Wall came down in 1989.
This was only the fifth competitive meeting between the clubs, following Union's promotion to the Bundesliga in May, having previously only met in Germany's second tier.
Among older fans too, the sporting rivalry replaced any nostalgic thoughts. At 48, Nicole Burckhardt experienced the fall of the Wall as a teenager.
“At my age”, she said, “I believe that history plays no part, for me it's all about football”.
Fellow Union fan Andreas Rudolf, 56, agreed the derby's background pales compared with bragging rights now secured.
“That was a long time ago, but we are two different clubs, one is blue, one is red” and both clubs wanted “to be number one today”.
“It's definitely not a friendship, but perhaps there's no hostility either, that has to do with” the past, but “we don't like them – the Blues.”
Union now leads the mini series with two wins with two draws, to a single Hertha victory, in competitive games.
Hertha hosted Union in a friendly at the Olympic Stadium in January 1990 — just days after the Wall fell — when both sets of fans united on the terraces to sing about Germany's imminent reunification – a unique moment some fans will never forget.
“It used to be that Hertha and Union were friends, which is important to us,” said 71-year-old Hertha fan Helmut Klopftleich, a former East German who fled to west Berlin in 1984.
“We lived in East Berlin at the time of the Wall, but ran away to the west, and moved from Union to Hertha.
“Today, we are real Hertha (fans)… and have been since 1984.”