Nadal had already qualified for the last four and his victory secured a first place finish in Group A of the prestigious season-ending event at London's O2 Arena.
Czech fifth seed Berdych could have gone through with a win, but instead he was eliminated and Swiss seventh seed Wawrinka progressed to the last four following his victory over David Ferrer earlier on Friday.
The Lausanne native lost the first set to Ferrer but came back to win in three sets 6-7, 6-4, 6-1.
"What can I say, I'm so happy right now," said Wawrinka, who ended 2-1 in group play.
"David is so tough and playing so well," he said following the match.
"I had to fight so much to get the win, but I'm really, really happy.
"This was so important for me."
Nadal's semi-final opponent on Sunday will either be Wawrinka's compatriot Roger Federer or Argentine fourth seed Juan Martin del Potro, depending on the winner of Saturday's Group B clash between those two.
Wawrinka, playing in the Tour Finals for the first time, will take on Group B winner Novak Djokovic in the other last four clash.
"Stan came to the locker room and said good luck," said Nadal.
"I said I would try my best," the Spaniard said.
"It's a good result for Stan," he said.
"He's good friend of mine," said Nadal.