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.
He played down any notion of getting one over on his former club PSV, who sacked him in March this year.
"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.
PSV remain top with 33 points from 14 matches, two ahead of Twente Enschede, who were held to a 2-2 draw by strugglers PEC Zwolle, and third-placed Vitesse.
Dusan Tadic converted a penalty shortly after the break to put Twente ahead but Denni Avdic equalised minutes later, netting a rebound.
Joey van den Berg scored from a free-kick two minutes from time to put Zwolle in front but Luc Castaignos salvaged a point for Twente with a well placed header in stoppage time.
Fourth-placed Ajax Amsterdam and fifth-placed Feyenoord reduced the gap on the leaders to six points as they registered away wins at Roda JC Kerkrade and AZ Alkmaar respectively.
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.
Feyenoord put on a solid performance in their 2-0 win at Alkmaar where 17-year old Tonny Vilhena put the visitors ahead midway through the second half with a fierce drive from inside the area.
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.
