Orient had won all seven of their League One games ahead of the trip across the capital and they made it eight out of eight thanks to a clinical second-half performance.
A David Mooney penalty midway through the second half and a Shaun Batt strike five minutes from time sent the ruthless leaders five points clear of the chasing pack.
Harlee Dean flashed a header wide of the far post for the hosts early on before Mooney's header flew over the bar for Orient.
Will Grigg wasted a glorious chance to open the scoring just before the hour mark when Adam Forshaw's low ball into the box found him in space at the far post but he could only scoop his effort wide via a deflection.
From the resulting corner, Clayton Donaldson managed to get ahead of his marker but he could only head into the arms of the keeper Jamie Jones.
But despite Brentford's dominance, it was Orient who took the lead through Mooney's 65th-minute penalty after he was pulled over in the box by Shaleum Logan.
Logan can have no complaints after man-handling Mooney inside the area before the Orient man tucked his penalty into the left corner and beyond Richard Lee.
Moments later, the visitors almost doubled their lead when the impressive Moses Odubajo found himself in space on the right side of the box and thumped a shot which Lee managed to tip over the bar.
Substitute Batt (85) had only been on the field a couple of minutes before he wrapped things up for Orient - neatly firing home left-footed after Odubajo's neat control and perfectly-weighted pass put him in the clear.