The victory for Bashar al-Assad's Russian-backed forces helps secure his grip on power just as the Republican president-elect prepares to swear off regime change and drop support for Syrian rebel forces.
Trump, a brash foreign policy novice who takes office on January 20, has already said he wants to reset relations with Vladimir Putin's Russia and to work with Moscow against jihadist threats.
He has also called into question the limited US backing for some of the rebels ranged against Assad, insisting Washington has "no idea" who it is dealing with and is better off without them.
"We will stop looking to topple regimes and overthrow governments, folks," Trump told a victory rally in Ohio this month, complaining that US wars in the Middle East have cost $6 trillion.
"Our goal is stability, not chaos," he said, in a nod to the fighting unleashed in Libya, Iraq, Yemen and Syria since the Arab Spring revolts.
"We will partner with any nation that is willing to join us in the effort to defeat ISIS and radical Islamic terrorists," he added, a clear call for closer cooperation with Russia.
America has been here before. Before the Arab Spring revolts, Washington aligned itself with strongmen, preferring stability over the promise of often Islamist-backed popular movements.
But in a June 2009 landmark speech in Cairo addressed to the Muslim world, Obama -- while vowing to fight violent extremism -- stood up for the region's struggling democrats.
- Syrian bloodbath -
"Suppressing ideas never succeeds in making them go away," he warned the region's authoritarian leaders, many of whom have since been ousted, unlike Syria's tenacious and brutal Assad.
The great hopes reflected in and fed by the Cairo speech have now largely been dashed.
Libya and Yemen are in chaos, Egypt has slid back into autocracy and Syria is a bloodbath.
America could walk away, but it has unfinished business with the Islamic State group, an Islamist faction with global ambitions holding a so-called "caliphate" in eastern Syria and northern Iraq.
After early stunning victories against hapless government forces, the jihadists have been rolled back in Iraq by US-backed local troops and in Syria by militias with US training and support.
Trump campaigned boasting that he had a quicker plan to "bomb the shit" out of the group -- and this now appears to be coalescing as a de facto alliance with Russia in Syria.
And, despite the difference in rhetoric between the outgoing and incoming administrations, the groundwork for such cooperation has already been laid by Obama's outgoing secretary of state.
Signup to our newsletter and follow us on Facebook and Twitter!
On September 9, John Kerry met his Russian counterpart Foreign Minister Sergei Lavrov in Geneva and signed an agreement to create a so-called "Joint Implementation Center," or JIC.
If a ceasefire were to take hold in the civil war, Kerry said, "we will see the United States and Russia taking coordinated steps to isolate and defeat the terrorist groups."
The JIC deal quickly fell apart amid anger after Russia bombed a UN aid convoy and US-led coalition warplanes accidentally hit a Syrian military unit, but Trump and Putin could now revive it.
US officials, European diplomats and expert observers now expect Assad to consolidate his control of the populous west of Syria with the help of Russia, Iran and Iran-backed militias.
Meanwhile, in a de facto division of the country into areas of responsibility, local militias with US special forces backing and air support will fight the IS group in the eastern desert.
"The real question is what the relationship will be with Russia, I think," Andrew Tabler, author of "In the Lion's Den: An Eyewitness Account of Washington's Battle with Syria," told AFP.
Assad now has fewer than 25,000 mobile troops which can be deployed away from their defensive positions, said Tabler, a fellow of the Washington Institute for Near East Policy.
Therefore, rather than taking the fight east to the Islamic State, Assad is likely to turn his attention to the northern city of Idlib, where rebels are already under Russian bombardment.
- Iranian militia -
"The first issue the Trump administration will look at will be to examine the possibility of implementing the Joint Implementation Group," Tabler said.
And Trump seems no less willing than Kerry to work with Russia.
His nominee to replace Kerry as secretary of state is ExxonMobil chief executive Rex Tillerson, a veteran oilman with close Russian ties who was awarded a medal of friendship by Putin himself.
One sticking point in Syria may be Washington's covert support -- separate from the avowed anti-IS fight -- for some of the rebel factions battling Assad, forces that have been bombed by Russia.
"This nominally is being pursued with the idea of overturning the Assad regime but it's primarily intelligence gathering and periodically putting pressure on the regime," Tabler told AFP.
"If they cut it off, and Trump has said he might, then you'd lose a lot of that intelligence."
After that, the last sticking point may be Iran.
While Trump's rhetoric and his cabinet roster suggest sympathy for Russia's role in Syria, nominees such as future defense secretary retired general James Mattis are staunch foes of Iran.
Assad may owe his survival, in part, to Russia's warplanes, but he is also dependent on the manpower provided by Iranian-trained and funded militia fights from Iraq, Lebanon and beyond.