Toni, revisiting the venue where in 2006 he captured the World Cup with Italy, struck in the 11th minute after being fed the ball by Frank Ribery, the France international who had opposed his teammate in the World Cup final.
That goal appeared to have decided the affair only for Dortmund's Mladen Petric to snatch an injury time equaliser, to force extra time.
But Toni, who like Ribery joined Bayern last summer, had the last word when he grabbed the winner in the 103rd minute. Bayern's win was the first leg of what they hope to be a treble.
They are sitting comfortable in the Bundesliga, 10 points clear of the chasing pack and face Saint Petersburg in the UEFA Cup semi-finals.
This was a final Cup appearance for Bayern talisman Oliver Kahn with the goalkeeper retiring at the end of the season.
For him it was a sixth Cup success. This final meanwhile had a special edge to it for Bayern coach Ottmar Hitzfeld as he had a seven year spell as manager of Dortmund.