The former Springbok back rower made no attempt to hide his disappointment at falling at the last hurdle for the second time in three years but he insists he is at least able to take some positives back to France.
"We gave our best. The boys showed a lot of heart out there," said van Niekerk, after Toulon had Carl Hayman and Steffon Armitage sinbinned in the second half of an ill-disciplined performance that saw Dimitri Yachvili slot seven penalties for Biarritz.
"We played with 13 men against 15 for a period of time and you cannot afford to give away yellow cards like that in a final.
"That made things really difficult but the boys hung in there - that's one thing we can take from the game.
"We kept the scoreline tight and we were still in with a chance right until the last minute of the game."
Toulon could have taken the match into extra time had they managed to engineer a drop goal opportunity for Jonny Wilkinson but the chance never quite came about in difficult conditions in South West London.
England's World Cup winning hero kicked Toulon into the final itself with a long-range drop with just 45 seconds remaining of the semi-final clash with Stade Francais and van Niekerk was hopeful a repeat would follow on Friday.
"Jonny was on song. He hit one drop goal over which was amazing," added van Niekerk.
"If we had given him an opportunity there, I'm sure he would have taken it. Maybe we took it one phase too many because that chance was lost.
"You can look at those small things but it's discipline that let us down. It was an uphill battle. But all credit to the boys they hung in there and showed a lot of heart."