The Dutchman has been awarded Wednesday's match at Signal Iduna Park after his fine performance in the quarter-final encounter between Barcelona and PSGBorussia Dortmund and Real Madrid.
The 40-year-old is seen as one of the top arbiters around in the game and has already refereed four matches in European club football's elite competition earlier this season, earning plaudits for his good performance in the second leg of the quarter-final tie between Barcelona and Paris Saint-Germain (1-1).
Kuipers was also active at Euro 2012 last summer, where he was in charge of the group-stage games between Ireland-Croatia and Ukraine-France.
The Dutch official was at the centre of attention last season when he awarded Barcelona a controversial spot kick in the Champions League match against AC Milan, but has never lost Uefa's trust.
The first leg of the other semi-final between Bayern Munich and Barcelona has been awarded to Viktor Kassai.