Antoine Dupont's stunning run from deep in France territory led to the breakthrough try for Willemse, with his team-mates moving the ball sharply when the captain was belatedly halted.
France worked the ball right to left for their next score, as Penaud and Cyril Baille each smartly offloaded when stopped short to allow Yoram Moefana to get over.
A strong Scotland response was rewarded with Rory Darge's try, and they should have had another when Chris Hogg failed to gather a routine pass on the counter.
Instead, France stretched their advantage heading into the break as Fickou powered over in the corner, and the bonus point was secured within two minutes of the restart courtesy of a generous bounce for Danty.
Les Bleus controlled the match from there and created opportunities for Penaud to get his name on the scoresheet twice, sauntering in for number five and then gathering a crossfield kick in plenty of space for their sixth and final try.
Duhan van der Merwe got a late Scotland consolation, although unlike when he crossed in the 85th minute in Paris last year, it was France who celebrated at full-time.
