Bangalore were in danger of falling to fifth on the table if they suffered a decisive loss, which would have allowed Kings XI Punjab to sneak through to the knockout phase on net run-rate.
But 19-year-old opening batsman Manish Pandey hit the second ton of the competition, paving the way to 170-4 after Bangalore won the toss and batted.
Deccan reached 158-6 off 20 overs in reply, falling short in their chase despite a valiant effort from Herschelle Gibbs, who returned to form by smashing 60 runs off 43 balls.
Deccan, bottom of the table in the first edition of the IPL last year, were already assured of a place in the knockout stages, but dropped to fourth as Bangalore leapfrogged them.
Chargers will face table-toppers Delhi Daredevils in the first semi-final in Centurion Friday while Bangalore play second-placed Chennai Super Kings the following day in Johannesburg.
The final will be played in the middle of an extravagant gala event at the Wanderers Sunday.
Bangalore won the toss and chose to bat, getting off to a good start in what was a crucial encounter for them.
Roelof van der Merwe paired with Pandey in a 55-run stand for the second wicket after opener Jacques Kallis made a second-over exit.
Van der Merwe was stumped by Adam Gilchrist off Andrew Symonds in the last over before the ´strategy break´, contributing 23 off 18 deliveries.
But Pandey, promoted up the order, batted through the innings, taking control as he smashed 114 runs from 73 balls with 10 fours and three sixes.
It was a remarkable effort from the little-known teenager, who took full advantage of being dropped on two by RP Singh to score only the second century of this Twenty20 extravaganza.
"It was a brilliant hundred," said Bangalore skipper Anil Kumble afterwards.
"Manish got a few opportunities but didn´t get to bat in the other games because he was batting lower down the order. So we just took a chance and sent him up the order and he came off really well."
In the first match of a double-header, Delhi got back on the winning trail with a four-wicket triumph over lowly Mumbai Indians.
Daredevils won the toss and chose to field with Mumbai reaching 165-8 as Dirk Nannes (3/27) spearheaded the Delhi attack.
And Delhi skipper Virender Sehwag made his first IPL half-century this season with 50 off 27 balls as they chased down their target with 15 balls to spare.
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