Centre-back N'Gala headed home a Ricky Holmes corner after four minutes to score his third goal of the season and steal the points.
In a busy afternoon for the big defender he was then lucky to stay on the pitch after a high and late lunge on Danny Hylton but referee Carl Berry deemed it only worthy of a yellow card.
It is the second home game in a row that the former Yeovil man has been the match winner and the result means the south-coast club are unbeaten in three league games.
Whittingham said: "We are seven points off the top and that is a good place to be. Of course we want to try and kick on for promotion as you want to be successful and that is our aim.
"Bondz had a good game for us and deserved his man of the match. He is attacking the ball well for us.
"We look at set-plays during the week and it's nice to see another one come off.
"With Bury having lost their manager in the week you always get a reaction and they reacted fantastically well for Ronnie Jepson, who will consider himself unlucky.
"We ground it out for sure and they will be disappointed."