The result means the Falcons are out of the Amlin Challenge Cup.
Openside Pennycook crossed the whitewash following an impressive break from Mark Wilson, to cancel out Mosese Ratuvou's early score.
Jimmy Gopperth slotted the conversion and then kicked the Falcons 13-7 ahead with a brace of penalties either side of half-time.
However, they failed to press home their advantage at Matmut Stadium, where Lyon responded with a penalty try converted by Romain Loursac before replacement Laurent Tranier stepped off the bench to cross for the home team's third try.
Newcastle had to win stand any chance of progressing.
In the end, though, their own result did not matter as Toulon gained the win they needed - 50-6 at Italian minnows Petrarca - to finish top of the group.
Former Falcon Jonny Wilkinson kicked nine points in Toulon's win, one which guaranteed them a home quarter-final.
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The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
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