Bony (53, 70) and Alfred Finnbogason (36, 63) cancelled out each other's efforts but Sven Kums' 74th-minute effort broke the pattern and gave the away side the lead.
Arnold Kruiswijk saw red for Heerenveen just three minutes later and Bony added his third from the penalty spot.
The point puts Vitesse level with FC Twente, having played one game more.
Heracles scored a 3-0 away win over second bottom PEC Zwolle, their second success of the season.
Samuel Armenteros got the ball rolling in the 14th minute before Ninos Gouriye took over with goals in the 68th and 81st minutes.
Roda JC also won 3-0 in their home clash against VVV Venlo.
Sanharib Malki was on target in each half, either side of Mark-Jan Fledderus' 54th-minute effort.
RKC Waalwijk drew 0-0 at Willem II.
The adidas Nitrocharge is the most talked about new cleat in years. It was released on May 15 and will take your pitch by storm.
Barcelona will wear this new home soccer jersey next season. They also have a new away jersey. Get them both.
The hoop soccer jersey is classic and cool. The USA hooped jersey is perfect for every fan. Get in the Gear.
Support the USA national team with an official 2013 Centennial soccer jersey from Nike. Its Official.
Neymar's move from Santos to Barcelona is no doubt the biggest summer transfer.
The Nike Hypervenom is the latest cleat silo from Nike. It will change your game and is worn by the game's top players.
Jamaica is in need of a win against the U.S. Get the jersey of the Reggae Boyz.
England will debut their new away jersey against Brazil at the Maracana Stadium on Sunday. Get in the Gear
Manchester City will try and win back the Premier League title with this new soccer jersey from Nike!
Germany is one of the top teams ever and they will play the US on Sunday.