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Clayton McMillan's side put in a messy performance hampered by missed tackles and handling errors to go down 19-15 in Bordeaux with several scuffles breaking out in the second half.
The Maori All Blacks levelled the match up at 8-8 shortly after halftime but that's as close they got to securing a second win of their short two-game tour.
Down 13-8, the Maori All Blacks were unlucky to be reduced to 14 men when Japanese referee Shuhei Kubo gave Jordan Manihera replacement a yellow card for clearing a French player out after the whistle. Replays clearly showed the tackle took place before Kubo called a stop to play.
With Manihera off the park the French Barbarians extended their lead to 19-8 heading into the final 20 minutes but another strange decision almost tipped the game towards the Maori.
Manihera returned to the field and darted down the blind side to set up Sean Polwart for a short run to the line but he was tackled high and was then held up over the line.
Antoine Tichit's high tackle was initially called just a penalty before Maori replacement captain Tim Bateman convinced Kubo to look at the option of a penalty try. After a TMO review Tichit was sent to the bin and the Maori were given seven points to close it to 19-15 and a one-man advantage for the rest of the game as boos rung around the packed ground.
However, the French Barbarians held up with some brave defence to secure the victory.
The Maori All Blacks opened their tour with a 51-9 thrashing of Canada in Vancouver last week.