GAIS looked the more likely to extend their unbeaten run in a first half which saw William Milovanovic and Robert Thorkelsson test Kristoffer Nordfeldt in the AIK goal, only for the home side to take the lead shortly after the break.
AIK put together a neat move down the left side, which resulted in Kevin Filling threading the ball through to Taha Ayari, who shrugged off his marker before slotting the ball past the goalkeeper.
Before the hour mark, the home side were in complete control when a ball was played through to Lukas Bergquist who had the simple task of squaring along the six-yard box for Filling to tap home.
The Mackerels seldom looked like getting back into the game, and they slip to seventh on goal difference, but a third win in a row sees AIK fly up the table into third for the time being.