Were all federal courts except the Supreme Court established by Constitutional Amendment since 1789?

No. Article III of the Constitution, which pre-dates all of the Amendments, mandated Congress create the US Supreme Court, and authorized them to establish other federal courts at their discretion. Lower federal courts are created, consolidated or disbanded by general legislation. The Judiciary Act of 1789 was the first such legislation, but it only created thirteen District Courts and three Circuits.

In addition to the US Supreme Court, the current federal court system includes 94 US District Courts and 13 US Court of Appeals Circuit Courts, as well as a number of limited jurisdiction tribunals, such as US Bankruptcy Court, US Tax Court, etc. The function and jurisdiction of the District and Circuit courts has both expanded and changed since the 1789.


Article III

Section 1.
The judicial power of the United States, shall be vested in one Supreme Court, and in such inferior courts as the Congress may from time to time ordain and establish. The judges, both of the supreme and inferior courts, shall hold their offices during good behaviour, and shall, at stated times, receive for their services, a compensation, which shall not be diminished during their continuance in office.

Section 2.
The judicial power shall extend to all cases, in law and equity, arising under this Constitution, the laws of the United States, and treaties made, or which shall be made, under their authority;--to all cases affecting ambassadors, other public ministers and consuls;--to all cases of admiralty and maritime jurisdiction;--to controversies to which the United States shall be a party;--to controversies between two or more states;--between a state and citizens of another state;--between citizens of different states;--between citizens of the same state claiming lands under grants of different states, and between a state, or the citizens thereof, and foreign states, citizens or subjects.

In all cases affecting ambassadors, other public ministers and consuls, and those in which a state shall be party, the Supreme Court shall have original jurisdiction. In all the other cases before mentioned, the Supreme Court shall have appellate jurisdiction, both as to law and fact, with such exceptions, and under such regulations as the Congress shall make.
The trial of all crimes, except in cases of impeachment, shall be by jury; and such trial shall be held in the state where the said crimes shall have been committed; but when not committed within any state, the trial shall be at such place or places as the Congress may by law have directed.

Section 3.
Treason against the United States, shall consist only in levying war against them, or in adhering to their enemies, giving them aid and comfort. No person shall be convicted of treason unless on the testimony of two witnesses to the same overt act, or on confession in open court.

The Congress shall have power to declare the punishment of treason, but no attainder of treason shall work corruption of blood, or forfeiture except during the life of the person attainted.