The former BVB defender has criticized the 45-year-old's handling of the Bayern-bound midfielder, claiming he returned to training too early which aggravated his injury.
The German prodigy was stretchered off with a hamstring complaint in the early stages of BVB's 2-0 defeat to Real Madrid in the second leg of their last-four tie at the end of April, only to be ruled out of the decider a month later.
However, the center back believes the coach is to blame for Gotze's absence at Wembley and subsequent spell on the treatment table as the attacking midfielder aggravated his knock in training five days before the final on May 26.
"Our coach was stupid. Mario felt a knock in the game against Real Madrid and was then taken to a Munich hospital," Santana said in an interview on ESPN Brasil.
"When he returned, the coach let him train on the Tuesday. He should not have done so because there was an important game on Saturday."
Santana has since departed Dortmund and joined Ruhr rivals Schalke. Gotze, 21, will represent Bayern next season, despite being expected to miss the start of the new campaign due to injury.