Brown had a brief spell on loan with City ten years ago, conceding five goals in his only first-team appearance.
On his return to Sincil Bank with Brentford, he endured an equally torrid time and was at fault for both of Lincoln's first two goals.
Brentford started well with both Alan Connell and Nathan Elder forcing saves out of young keeper Ayden Duffy.
But Lincoln soon settled down and were unlucky in the 28th minute when Louis Dodds' 20-yard shot left Brown completely beaten but the keeper was saved by the post.
Lincoln went ahead six minutes before the half-time break with an almost comical goal. 18-year-old Gary King sent in a seemingly harmless cross from the left which bounced in front of Brown. The keeper then completely misjudged the flight of the ball and allowed it to bounce off his body and trickle into the net.
Brentford levelled in first-half stoppage time when the Lincoln defence was caught out by a ball into the box by Kevin O'Connor. As both centre-backs hesitated, Elder pounced to head in from close range.
Duff kept Lincoln in the game with an excellent 49th-minute save to prevent Glenn Poole from scoring.
But, after a bizarre booking for Paul Green who was yellow-carded for taking a free-kick too quickly, Lincoln went ahead.
Jamie Forrester was brought down on the edge of the box as he was about to shoot. The veteran striker picked himself up and fired the free-kick over the Brentford wall and past the badly-positioned Brown.
Lincoln went on to add a third goal in the 83rd minute when a cross from Green was headed in by Lee Frecklington.
The Red Imps could have increased their lead in stoppage time. King beat three defenders before being tripped by Matt Heywood.
Substitute Owain Warlow smashed a 20-yard free-kick towards goal, but Brown pulled off a fine diving save.