Victory in European rugby's second tier competition was just about deserved for the Basques, who will next season play in the main Heineken Cup, but Toulon fought hard in an often dour game at London's Stoop devoid of tries.
Neither side showed any real endeavour to reach the line in the first half and the boot of Yachvili and rival Jonny Wilkinson made the score 12-9 to Biarritz at halftime.
The second half livened up and Biarritz looked to have pulled clear, especially when Toulon were briefly reduced to 13 men when Carl Hayman was sin-binned on 46 minutes and then Steffon Armitage was yellow-carded for coming in from the side, allowing Yachvili to slot Biarritz six points ahead.
Toulon, beaten by Cardiff in the 2010 final, battled back and a trademark Wilkinson drop goal on 66 minutes pulled his side level at 18-18 but the 2003 England World Cup winner was later short with a long penalty.
Yachvili, lucky to avoid a yellow card, sent over a tricky-looking 74th-minute penalty to make the difference with his seventh successful kick from seven and a late drop goal chance for Wilkinson was denied when Toulon committed a penalty.