A crowd of 329 at the King George`s Field saw the Isthmian League Premier Division side take a 26th-minute lead after there had been chances at both ends.
Jason Banton`s cross was fired home in off a post by Gus Sow.
Boro `keeper Dante Baptiste saved well from Elliott Buchanan and then from Banton before the latter doubled the hosts` lead 3 minutes before half-time with a deflected looing effort that went over Baptiste.
Kingstonian started the second half where they left off and made Farnborough`s task a massive one when they added a third just 7 minutes after the break when Daniel Ajakaiye made the most of a couple of rebounds to net.
The visitors did manage to pull a goal back after 79 minutes with sub Harry Cooksley the scorer.
And shortly afterwards, K`s keeper Rob Tolfrey saved well from Paul Hodges to prevent the tie from getting interesting.
But it was the home side who had the final say when, 2 minutes into stoppage time, Buchanan was rewarded for a fine individual performance when he netted from close range after good work from Jay Barton.
So, Farnborough bowed out and can now concentrate on their promotion push, but they were beaten by a very decent side on the day.
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