Matt Mcilroy put Penryn a goal up before Dan Richardson equalised for the home side.
But a brace from former Falmouth player Bobby Bryant gave Penryn a two goal lead.
And despite pulling one back thanks to a second Dan Richardson goal from a penalty rebound, Penryn were able to hold on for all three points.
Elsewhere Paul Murray's Wendron side continued their good run of form with a convincing 3-0 win over Falmouth Athletic.
The victory moves Wendron into seventh position in the table, and inches them ever close to Murray's goal of a top six finish this season.
Saturday's Jolly's Combination League results were as follows:
Falmouth Athletic DC 0 - 3 Wendron United
Falmouth Town 2 - 3 Penryn Athletic
Hayle 0 - 1 Perranwell
Holman Sports Club 0 - 7 Ludgvan
St Agnes 0 - 0 St Ives Town
St Just 4 - 2 Mullion
Troon 1 - 2 Pendeen Rovers