It is derived from the Latin term Deus Ex Machina, meaning "God from a machine." It is a reference to the plot in the first game, in which Bob Page seeks to use nano-augmentations to essentially become God.
Or else it may be interpreted in the context of a plot device. A Deus Ex Machina is a character/device/ability/etc. that typically comes out of the blue or from under the antagonist's nose (not literally) that brings about a solution to a seemingly unsolvable problem. In Deus Ex, JC Denton is a deus ex machina. Page creates him, has him trained, then is killed by him. In Deus Ex Human Revolution, Adam Jensen is not. He is simply the protagonist.
Before the last boss fight, Zhao's remote control is a deus ex machina. No-one knows of it's existance until she tries to deactivate Adam's augmentations. However, it isn't a deus ex machina if Adam doesn't take the new biochip.