"To be an American diplomat is a high calling," Shannon said in a letter to his fellow employees, telling them that it was time to "step aside" and decide what to do with the rest of his life.
"I do so confident in the next generation of Foreign Service leadership, and proud of what we have accomplished across four decades of American diplomacy," he wrote.
In an interview with the Associated Press, Shannon said he was retiring for personal, not political, reasons. He cited his 60th birthday last week and the death of his mother late last year.
He also characterized himself as the "designated survivor" after he became undersecretary in February 2016. It was Shannon who met Tillerson at the door to the State Department when Tillerson first arrived a year ago Friday and escorted him to the stairway to address gathered employees.
Tillerson, in a statement he wrote by hand en route to a speaking engagement in Texas, lauded Shannon as an inspiration to his colleagues.
"I particularly appreciate his depth of knowledge, the role he played during the transition — as Acting Secretary of State during my confirmation and later as Acting Deputy Secretary — and his contributions to our strategy process over the past year," he said.
Shannon is a "career ambassador," a title conveyed on only a handful of the most accomplished diplomats. He had served as an ambassador to Brazil and also was posted to Venezuela, Guatemala and the Organization of American States. His career spanned six presidents and 10 secretaries of state.
His departure comes as the State Department faces deep budget cuts and has been sidelined by the White House on some of the most significant foreign policy endeavors, such as promoting peace talks between Israel and the Palestinians.
Although the total number of employees has not diminished significantly from a year ago, the State Department has suffered a brain drain of experienced and respected diplomats. Some have left for personal reasons. But others made clear they were pushed out or resigned because they could not support the Trump administration's "America First" foreign policy. Morale remains low among many remaining employees, and Shannon sometimes privately counseled some of them.
Shannon, who said he will stay on until a replacement is named, leaves behind a hole in the leadership team around Tillerson. A former ExxonMobil executive with no diplomatic experience when he arrived a year ago, Tillerson leaned heavily on Shannon for sensitive missions. Shannon was instrumental in sometimes adversarial talks with Russia and Venezuela. In December, he led the U.S. delegation to a meeting on the Iran nuclear deal, at which he talked to Iranians on the sidelines, urging them to release Americans considered wrongfully imprisoned as alleged spies.
"Tom Shannon is as skillful and decent a colleague as I've ever known," said William Burns, a former deputy secretary of state. "His departure, at a moment when American diplomacy is challenged abroad and undermined at home, is a real loss."
The State Department website quickly racked up accolades to Shannon from his fellow diplomats.
"He made us a better institution, and we are grateful and proud to have served with him," wrote Francisco Palmieri, the assistant secretary of state for the Western Hemisphere, a position Shannon once held.
State Department spokeswoman Heather Nauert called Shannon "a patriot, a diplomat and a great American." Steve Goldstein, the undersecretary for public diplomacy, described the staff and Tillerson as saddened.
"The secretary is as regretful as everyone else but we respect the decision he has made," Goldstein said.