"There were several times when I said to all of the parties involved that 'this is too important, this has to be seen through, you have come too far,'" the chief US diplomat recalled afterward on the plane from Zurich to London.
A last-minute hitch had raised doubts over whether Armenia and Turkey would follow through on two years of roller-coaster negotiations to finally sign documents in Zurich on Saturday to normalise ties and open their shared border.
Shortly after 5 p.m. Saturday evening, everything seemed in place for the two sides to mark a first step to reconciliation after a century of hostility over World War I-era massacres.
With her traveling press corps in tow, Clinton's motorcade arrived at the University of Zurich for the ceremony where foreign ministers Edouard Nalbandian and his Turkish counterpart Ahmet Davutoglu would sign the deal.
Suddenly, the motorcade turned tail and sped back up the hills to the Dolder Grand Hotel. Nalbandian had balked at signing the deal because he had concerns about a statement his Turkish counterpart would read, US officials said later.
It was the start of a three-hour mini diplomatic roller-coaster.
Initially, Philip Gordon, assistant secretary of state for European and Eurasian affairs, and Swiss official Michael Ambuehl met with Nalbandian inside the hotel, US officials told reporters.
They shared his concerns with the Turkish delegation, which eventually dispatched a diplomat with a revised version of the statement Davutoglu planned to read, the officials added.
As if to heighten the drama, the diplomat arrived inside a brightly-painted Swiss police car, its sirens wailing and forcing reporters to step out of the way.
But there appeared to be no progress.
Gordon emerged later from his meeting with Nalbandian and joined Clinton -- who had met earlier in the day with both the chief Armenian and Turkish diplomats -- inside the BMW sedan in a driveway at the rear of the hotel.
Clinton used different cellphones inside the car to speak to both the Turkish and Armenian foreign ministers, a senior State Department official told reporters on the condition of anonymity.
There were also calls to the Swiss mediators and other diplomatic players.
The pair finally emerged after what seemed close to an hour inside the vehicle. Clinton joined Nalbandian in the hotel and the pair soon returned to the car together and headed to the university
But it then took around another 90 minutes before Nalbandian and Davutoglu re-emerged from the university walls and entered the ceremonial room to sign page after page of documents.
Nalbandian remain stern-faced while signing, but Davutoglu smiled at times.
The two ministers and US, Russian, French, Swiss and EU counterparts immediately left the room instead of making scheduled statements, in an agreement to bypass the hitch, diplomats said.
Relations between NATO member Turkey and Russian-backed Armenia have been severed since the World War I mass killings of Armenians under Ottoman rule.
The bridge-building by the two governments after more than a year of discreet Swiss-mediated talks is still hampered by fierce opposition from critics at home.
Clinton expected there to be more bumps ahead as the documents have to go before the parliaments of both countries and acknowledged the courage of the two top diplomats.
"When you're trying to help people resolve longstanding problems between themselves, it is a very challenging process," she said, citing the weight of history and domestic political opposition.
She acknowledged in particular how hard it was for Nalbandian.
"He had really deep concerns and wanted to make sure people understood them," Clinton said. "We conveyed that we not only did understand but appreciated how hard this was, but that this needed to be done."
Clinton added that Nalbandian had to call his president Serzh Sarkisian several times to consult on the issues.
A senior US official told reporters on the condition of anonymity that President Barack Obama telephoned Clinton as she left for Zurich airport. "He was very excited. He felt like this was a big step forward."