The butcher, who specialises in organically-raised meat, was at his stall in the covered Saint-Quentin market in the north of the capital when it was targeted on Saturday.
“I was preparing a client's order. I felt liquid hit me, I touched my head and the liquid was quite red,” the butcher told BFM television.
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“I looked up and there were 15 or 20 people in front of the stand with the slogans 'Freedom and defence for animals',” he said.
The two suspects were to be brought before a judge to face potential charges later on Monday.
A series of French butcher shops have been vandalised in recent months by “anti-speciesism” activists, who say eating meat is an immoral violation of the rights of other species.
Last month a court in northern France handed jail terms to two vegan activists for a string of attacks on butchers, shops and restaurants selling meat.