Town did well in the first half, but the absence of two key players proved too much of a handicap as Godalming, having a good season, stepped up the pressure in the second 45 minutes.
Danny Brown and Gareth Slessor were both ruled out by injury and it was the pace at the back provided by Brown that Farnham missed in particular.
Graeme Miles, playing as an emergency centre-back, had a solid game and the visitors held firm in the first half after they had got used to the inadequate lights at Weycourt.
And Farnham were good value for a 0-0 score at half-time. New goalkeeper Mike Brawley, a County U/18 player, signed from Westfield last week, made two superb saves, but Alan Morgan and Kevin Annetts also went close at the other end.
It was Mick Nolan, recently signed from Chipstead, who made the breakthrough on the hour, just six minutes after coming on as substitute. Picking up Shaun Lydon's pass, Nolan ghosted past three Town defenders and beat the advancing Brawley.
Farnham's concentration wavered. Ten minutes later, Mick Flynn flicked on a free-kick and another substitute, Glen Stanley, drilled home at the far post.
Farnham fought back with five corners in quick succession and Annetts had a header cleared off the line.
But the Nolan-Lydon combination struck again in the final minute, giving Godalming an emphatic margin of victory. Nolan provided the cross and an unmarked Lydon fired home his 27th goal of the season.
"I was proud of my players and how they handled the situation on Saturday, but the second half at Godalming was a case of After the lord Mayor's Show," said manager Dave Ward. "We silenced the crowd at Wimbledon and in the end everyone was complimenting us on our performance. The changes we had to make for Godalming obviously affected the side."
And his opinion after seeing two of the top sides in the space of three days? "Withdean are a bit special and clearly have Ryman League potential. I think Wimbledon still have a way to go."