The Brazilian's car failed a post-race examination on Saturday evening, hours after the race, where it was discovered the front wing had been reinforced and six of the eight holes in the piece had been filled.
Di Grassi's Audi Sport ABT team argued the changes were made due to repairs and offered no competitive advantage, but organisers upheld their decision and Di Rossi's team will not appeal.
It means that second-placed Belgian Jerome D'Ambrosio, who had finished more than seven seconds behind Di Grassi over the 33 laps, is now officially the winner of the Berlin ePrix.
And Nelson Piquet Jr, son of the former Formula One star with the same name, takes over the lead in the drivers' championship, 10 points ahead of di Grassi, having been moved up from fifth to fourth in Berlin.
For D'Ambrosio, a former Formula One driver with Virgin, it is his first victory on the Formula E circuit after eight races.
Launched this season, the series features 100 percent electric cars competing over 11 rounds and there are three races left, including Moscow on June 6 and the season finale with two races in London on June 27 and 28.
Original source: Formula E winner gets disqualified