Both goals came in the space of a minute midway through the first half.
Town created as many chances as the home side, but it was the same old story of poor finishing in front of goal.
The visitors could have taken an early lead, Graeme Miles sidefooting wide from close range.
Then Farnham, who defended pretty well in general, paid for a brief lapse of concentration.
On 22 minutes, they failed to clear their lines and James Blason managed to get in a cross that was headed in at the far post by Shaun Elliott.
A minute later, Farnham gave away possession and Shaun Lydon found the far corner with an angled shot from some 20 yards.
The visitors were unlucky not to hit back in a strong finish to the half. Vince Decicco's drive was blocked on the goal-line by Paul Jones and a long-range shot from Gareth Slessor was tipped round the post by Dave Tidey at full stretch.
Kicking down the slope in the second half, Farnham had most of the possession, but rarely troubled goalkeeper Tidey.
The Godalming attack carried the greater threat and twice Chris Edmonds made good saves to deny Lydon, while Jason Blake cleared off the line from Mick Hudson.
At the other end, Miles was clear on goal after combining well with Alan Morgan, but Tidey was equal to the shot.
Farnham: Edmonds, Hatton, Slessor, Blake, Decicco, Moore, J Brown (Snowden), Hooper, Miles, Morgan, Williams (D Brown). Sub (not used) Brooks.
Farnham have no fixture this Saturday, but on Tuesday they are home to Hartley Wintney in the Aldershot FA Senior Cup (ko 7-45 pm).
The winners will earn a home semi-final against Ash United who beat a Farnborough XI 2-1 on Tuesday.
Jamie Horton scored against his former club and Scott Joyce made it 2-0 before Rocky Baptiste pulled one back for the Conference club.
Farnham are planning a reunion for all former Town players on Saturday, April 20. For more information, ring the Farnham clubhouse on 01252 715305.