Whipp (21), Wearne (74)
Town dominated the opening exchanges. Rob Wearne had a goal ruled out for offside before Tom Whipp opened the scoring in the 21st minute when he latched on to Dan Richardson's cross and rifled an unstoppable half-volley into the top corner from the edge of the box.
But Penzance rallied and never allowed Falmouth to settle.
Harry Corin went close with a shot from 15 yards out, and only the linesman's flag prevented the Magpies from drawing level when Callum George was adjudged to have pushed a Falmouth defender before nodding in from close range.
After half time the game opened up, wth both sides squandering goal-scoring opportunities.
Pat Shaughnessy fired wide from a tight angle, before Whipp blazed over from 12 yards out after Wearne had played him in on goal.
Falmouth looked uncomfortable under pressure, but continued to pose a threat going forward, with Shaughnessy and Wearne combining well up front, and Richadrson and Whipp looking dangerous in midfield.
With 15 minutes left Wearne received the biggest cheer of the night after he reacted quickest to a loose ball in the box to slide in and score Falmouth's second.
The points looked secure for Town, but five minutes from time an unmarked Jeremy Blake fired a superb volley into the top corner to set up a frantic finish.
But despite putting Falmouth under plenty of pressure, the home side managed to hold on and secure the win for a visibly delighted Les Gilbert and Robbie Stephens.
Falmouth: Chapman (c); Holland, Kellow, Floyd-Norris, Webb, Jeffrey; Richardson, Pope, Whipp; Wearne, Shaughnessy
Penzance: M. Williams; Best, R. Williams, Mooney, Andrew; Street (c), Corin, Wills, Blake; George, Andrew