Midfielder Malone set the game alight in the 20th minute with a wonderful weaving solo effort that handed the Cherries a deserved first-half lead.
Picking the ball up just inside the visitors’ half, Malone surged past four Scunthorpe challenges before rolling the ball into the bottom right corner past Scunthorpe goalkeeper Sam Slocombe.
But Alan Knill’s side could easily have found themselves level just moments after the restart as the industrious Chris Dagnall flashed the ball agonizingly across the Bournemouth box.
It was from that point that the Iron began to assert their control on the game and had further chances to level at the start of the second half, in particular through Michael O’Connor, who fired into the side netting.
But Lee Bradbury’s side were not to be denied the three points as Thomas pounced on some defensive indecision to drive home a decisive second in the 73rd minute.