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As Supreme Chancellor, Palpatine was the head of state of the Galactic Republic. Since the Jedi functioned as a peacekeepers for the Republic, they were bound by its laws. Palpatine could exercise legal and political power over the Jedi Order. (The Jedi didn't know that their head of state was a Sith Lord at the time.)

Did any other Sith ever exercise political, legal, or organizational power over the Jedi Order?

Palpatine once told Anakin, "Once more the Sith will rule the galaxy". Did those ancient Sith who ruled the galaxy also have legal power over the Jedi?

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I would say No.

It was only after the Jedi Order built the Temple on Coruscant and moved their headquarters there in 5,000 BBY that they came into the service of what was The Old Republic.

Between then and 1,000 BBY, the only instance I can find is the signing of the Treaty of Coruscant in 3653 BBY, where Darth Baras forced the Republic and the Jedi Order to end the Great Galactic War by ceding a lot of outlying territories and dissolving old alliances. However this was a treaty signed to end an open war, not subterfuge like Palpatines, so I'm not sure if you would count this.

Sith were thought extinct from 1,000 BBY, which led to complacency by the Jedi Council. This is also the year Darth Bane established the Order of the Sith Lords, and the Rule of Two. Of the Dark Lords that are known between Bane and Sidious, none of them had anything to do with politics, except Darth Tenebrous, who was a legendary starship designer known as Rugess Nome, and his apprentice Darth Plagueis, whos public persona was Hego Damask II.
Plagueis inherited a banking clan from his father and set up a financial lobbying group of his own. The pair used their connections and power to influence galactic politics, but not the Jedi.

Plagueis was the one that trained Palpatine when he discovered him on Naboo as a young aristocrat. You could argue that Plagueis exercised political power over the Jedi in the events of Episode I, but, while it was his plan, Sidious was the actual puppet master.

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