The incident occurred on Tuesday evening, outside the Ohr Torah school where Merah shot dead a rabbi and three children on March 19, 2012.
The student, who fled back into the school, was not hurt and the woman turned out to be a well-known local with a history of psychiatric problems.
But the confrontation nevertheless served to underline the sense of insecurity that haunts the community as the first anniversary of the attack approaches.
"Fear is everywhere," said Arie Bensemhoun, the chairman of Toulouse's Jewish community. "With every passing day we become more convinced of this: that Mohamed Merah, there was not just one of him."
Nicole Yardeni, the regional head of the Jewish representative group CRIF, said: "There is no doubt this was an anti-Semitic act, even if you have to distinguish between anti-Semitic mania and acts with an ideological objective."
The Ohr Torah school is better know by its previous name, Ozar Hatorah.