Victory for seventh-placed Biarritz sees them close the gap on Grenoble in sixth to two points, although Grenoble will have the chance to move ahead again when they meet Castres on Saturday.
Agen remain third from bottom, with 18 points from 15 games this season.
Opeti Fonua touched down for Agen while Anthony Hegarty responded for the hosts. Julien Peyrelongue's kicking proved the difference between the two sides.
The visitors will have been encouraged by their performance on the Atlantic coast though and depart with a well deserved defensive bonus point. It might even have been much different, after they dominated play during the final 15 minutes.
But Biarritz did what they had to do to secure back-to-back victories and remain in the hunt for the play-offs.