After a scoreless first half at Parc des Sports Aguilera in which Owen Farrell and Marcello Bosch missed chances with the boot, the game burst into life following the interval with the hosts grabbing tries through Imanol Harinordoquy and Takudzwa Ngwenya.
Saracens fought back and secured what could be a vital losing bonus point when Alex Goode squeezed into the corner with the last play of the match following a sustained period of pressure.
Saracens director of rugby Mark McCall was upset his side were unable to secure an historic win at Biarritz as they fell to a third defeat in the Basque country, but he was pleased to see his side remain in the contest and get some reward at the end.
He said: "We're very disappointed to have lost, we never like losing, but the history of this competition shows you have to come away with something.
"At 15-3 down in France, with a vocal crowd behind their team, it is easy to fold but we didn't and we could have scored more tries.
"We showed a lot of character and skill in that final quarter to come away with the try. The rules of the competition state that if we finish level it goes to the head to head between the two teams - so the bonus point could be important at the end of the pool stages.
"It was a very physical match. This competition means everything to Biarritz - this is their season.
"Our set-piece didn't function as well as it normally does and we were under a bit of pressure in that area.
"We were disappointed with the tries they scored. They were two long-range tries where we lost concentration having not been under pressure."
Saracens still top Pool Five thanks to their maximum points haul against Benetton Treviso last weekend and next face the Ospreys in a December double-header.
McCall reckons the clashes with the Ospreys could make or break his side's Heineken Cup ambitions.
He said: "The double-header is really important. The Ospreys have had a good domestic season so far and I watched them against Biarritz last week, where they did very well.
"They will be two huge matches and whoever comes out on top will have a big say in how this group finishes."
Meanwhile, Biarritz tryscorer Ngwenya admitted his side breathed a sigh of relief after recording their first victory of their European campaign following last weekend's 28-21 loss at Ospreys.
Ngwenya said: "It was good to get the win and score a try especially after last week. It was important that we won, you have to win your home games.
"But it was devastating to give away a try at the end - that could be crucial in terms of qualification. We face Benetton Treviso next and have to win both games and secure as many points as possible."
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