Timothy Derijck put PSV ahead after five minutes, netting from close range after the Vitesse defence failed to clear a free-kick, but 10 minutes later former PSV striker Jonathan Reis equalised when he fired his free-kick through the wall.
PSV dominated the match and created the better chances but as Vitesse held firm, their reward came 16 minutes from time when Theo Janssen reached Reis, who headed the ball back for Bony to score his 15th goal of the season.
"PSV had the better chances but that doesn't make our win less sweet," Vitesse coach Fred Rutten told reporters.
"But that has nothing to do with this match. I am not interested in that sentimental stuff and it was not about me today," he said.
Ajax had to come from behind in their 2-1 victory after Guus Hupperts opened the scoring for Roda with a long drive after 14 minutes but in the final eight minutes Danes Christian Eriksen and Lasse Schone made the difference for Frank de Boer's men.
Alkmaar's Dirk Marcelis was sent off six minutes from time after a wild tackle on Jean Paul Boetius and shortly afterwards Ruben Schaken settled the match with a shot from 18 metres.
