Exeter threw away victory after conceding a penalty in the dying stages.
Steve Flack put the Grecians ahead with a powerful header on the hour mark. At that stage they were well on top but Exeter allowed struggling Farnborough back into the game and paid the ultimate price when Leroy Griffiths scored from the spot.
James Coppinger had the first shot of the game after quarter of an hour for Exeter, but his strike from the edge of the box was well saved by Mark Osborn.
Farnborough's best early effort came through a long range strike from Adie Hayes which was comfortably held by James Bittner.
Exeter began to look more dangerous as the half wore on and Reinier Moor's long-range effort was held by Osborn.
Coppinger was constantly a threat for Exeter. He forced Osborn to save well with another long-range shot.
Just before half time Osborn leapt superbly to keep out Alex Jeannin's header.
Exeter should have taken the lead ten minutes after the restart. Coppinger's cross was nodded back by Flack and Martin Thomas headed over the bar from only six yards.
Thomas then shot into the arms of the goalkeeper from the edge of the box as Exeter piled on the pressure.
It finally told on the hour mark. Jeannin's deep cross from the left was met by Flack and his bullet header flew past Osborn. The goal was no more than Exeter deserved.
Farnborough attempted to get back into the game. In the dying minutes Flack could have increased the scoring but his shot from 12 yards was saved by Osborn.
But with three minutes on the clock Barrington Belgrave powered into the box and was brought down by Bittner as he attempted to dribble past the goalkeeper.
Griffiths fired home the penalty to earn his side a point. In injury time Jeannin was shown red for his second bookable offence.