Former RB striker Selke grabbed a brace on his return to Leipzig, as Hertha battled to an astonishing triumph, despite going down to 10 men early in the game.
Selke curled in the opener for Hertha in the fifth minute, but his joy was short-lived as Hertha defender Jordan Torunarigha was controversially sent off for colliding with Timo Werner just minutes later.
Hertha refused to buckle, and Salomon Kalou doubled the lead with a powerful header on the half-hour mark.
Five minutes after the break, Selke was denied by goalkeeper Peter Gulacsi on the counter-attack, only to score at the far post from the resulting corner.
Not until the 68th minute did Leipzig strike back, with Willi Orban heading in a cross from Bruma.
Marcel Halstenberg then headed in a long ball in injury time, but it was too little, too late for an exhausted RB side.
Leipzig have failed to win any of their four league games this month, and have now dropped to fifth in the Bundesliga table, level on points with fourth-placed Bayer Leverkusen.
In Sunday's other game, a Leon Bailey double was not enough for Leverkusen as they were held to a thrilling 4-4 draw in Hanover.
Substituted on at half-time with his team trailing 3-2, Bailey scored twice to put Bayer on course for victory, but Julian Korb's equaliser saved a point for Hanover.
Julian Brandt put Leverkusen ahead with a brilliantly controlled volley on 11 minutes, only for Ihlas Bebou to immediately head Hanover level at the other end.
Niclas Fuellkrug's penalty then put Hanover in front, before Admir Mehmedi's well-angled shot levelled the scores once more.
The drama continued just before half-time, as Hanover struck on the counter attack, Felix Klaus whipping in a fine shot to restore the lead.
Leverkusen coach Heiko Herrlich brought on Bailey at the break, and the move immediately paid off, as the Jamaican broke down the left wing and made it 3-3 two minutes into the second half.
Bailey struck again 20 minutes later, putting Leverkusen into the lead with another devastating counter-attack on the left flank.
However seven minutes from time, sloppy Leverkusen defending allowed Korb to squeeze in Hanover's fourth and rescue a well-earned point for his team.
"It was a crazy game, with both teams fighting from the first minute," Bailey told Sky Sports. "We should have come out victorious, but we were not focused enough in front of goal."
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