Aishah Azmi, 23, was asked to remove the veil after the school in Dewsbury, W Yorks, said pupils found it hard to understand her.
Kirklees Council was ordered to pay her £1,100 for victimising her.
The tribunal dismissed her claims of religious discrimination and harassment on religious grounds.
Ms Azmi said she was considering an appeal against the decision to dismiss three of her claims.
In a statement she criticised ministers who had intervened in the case and said it made her “fearful of the consequences for Muslim women in this country who want to work”.
She said: “However, I am pleased that the tribunal have recognised the victimising way in which the school and the local education authority have handled this matter and the distress that has caused me.”
The case attracted comments from Prime Minister Tony Blair, who backed Kirklees Council for suspending Ms Azmi.
Mr Blair said the wearing of a full face veil was a “mark of separation” and made some “outside the community feel uncomfortable”.
Ms Azmi said: “Muslim women who wear the veils are not aliens, and politicians need to recognise that what they say can have a very dangerous impact on the lives of the minorities they treat as outcasts.
“I will continue to uphold my religious beliefs and urge Muslims to engage in dialogue with the wider community, despite the attacks that are being made upon them.”
Headfield Church of England Junior School suspended Ms Azmi because it said pupils found it hard to understand her during lessons.
Kirklees Council said the decision “had nothing to do with religion” but was about ensuring pupils get the best education possible.
But Ms Azmi said the veil caused no problems with the children, with whom she had a “brilliant relationship”.
She said she would remove the garment, but not in front of male colleagues.
Dewsbury MP Shahid Malik said the decision to reject her claims of religious discrimination was “a victory for common sense”.
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