A goal by striker Didier Tholot a minute after the interval was enough for the French side who had also won the first leg of the semi-final 1- 0 in the Czech Republic.
The match failed to reach the heights of Bordeaux's stunning 3-0 quarter- final win over Milan, after they had lost the first leg 2-0 in Italy, but the French club were rarely troubled by the Czechs on the way to their first European final.
It was Bordeaux's 18th match of the season in Europe, including the Intertoto fixtures which gained them entry into the competition.
The result ended an 18-year wait for France to have a team in the Uefa Cup final. The only previous French team to achieve the feat was Bastia in 1978.
In the two-leg finale, they will face Bayern Munich, who produced a surprise 2-1 victory in Barcelona's Nou Camp stadium for a 4-3 aggregate victory. Marcus Babbel and Marcel Witeczek put Bayern 2-0 ahead before Ivan de La Pena pulled one back for Barcelona in the 88th minute.
Ajax go into today's European Cup semi-final second leg against Panathinaikos in the Olympic stadium in Athens trailing 1-0 and without their injured striker Patrick Kluivert.Reuse content