Scunthorpe boss Brian Laws gambled with his selection because of suspensions and injuries but it didn't really pay off.
There was a lively start with Paul Brooker breaking through only to be flagged offside.
Scunthorpe's reply came from Andy Keogh who fired a low shot at Stuart Nelson who grabbed the ball just in front of Billy Sharp.
The home side broke the deadlock in the eighth minute. Richard Ryan's right-wing corner was flicked on by Keogh and Jim Goodwin rose well to head home.
The Bees responded almost immediately when Brooker floated in a free-kick which was not cleared properly and the ball fell to Pratley whose superb strike from 25 yards gave Paul Musselwhite no chance.
Brentford then capitalised a second time in the 24th minute. Jay Tabb knocked in a free-kick from the right which Musselwhite punched out straight to the feet of Pratley who struck a firm shot low into the net.
Scunthorpe improved towards the interval to force three successive corners, the last of which saw Nelson flapping at a Goodwin header which was eventually cleared.
The Bees made an immediate impact after the interval as Tabb got in a diving header which bought a brilliant reaction save from Musselwhite.
But the keeper could do nothing about the third goal in the 52nd minute when Brooker initiated the move before scoring.
At this point the game had slipped away from Scunthorpe's grasp and Musselwhite made two further excellent stops from Pratley and DJ Campbell.
Frustration eventually got the better of Goodwin who, after a yellow card in the 77th minute, was shown straight red three minutes later as the Iron slipped to their third successive defeat.