It was not a tarrif (sic)but an outright trade embargo with England and France.
Very good. And if you look at the constitution, tariffs and embargoes are two VERY different things. Tariffs fall under the Revenue Clause and therefore (according to the theory Jefferson applied, at least) must serve a primary revenue function as a domestic fiscal policy. Embargoes fall within the jurisdiction of foreign policy under the Commerce Clause, and serve a military/diplomatic purpose as was the case with the Napoleonic War embargoes of the late Jefferson administration.
Put another way, an embargo by its very definition has clear constitutional sanction as an uncontested power of the federal government. A tariff may or may not, depending on its use for revenue. And according to the Jeffersonians, only tariffs that were designed to produce revenue met constitutional muster whereas those that were designed to protect domestic industry did not.