Many of Donald Trump’s foreign-policy views shifted throughout the campaign, and the president-elect remains unpredictable. But Mr. Trump’s instincts on Syria may augur a viable alternative to the Obama administration’s failed strategy.

President Obama’s approach—with its focus on defeating Islamic State and displacing Syrian President Bashar Assad simultaneously, while devoting few American resources to the tasks—has failed to stop or even contain this humanitarian disaster. Since the Syrian civil war began in 2011, half of the country’s prewar population has been displaced and nearly 500,000 have been killed. The conflict provided a sanctuary for ISIS that it used to take a quarter of Iraq and to catalyze attacks on Western targets. ISIS is losing ground, but it and the country’s al Qaeda affiliate are far from defeated, and the war remains far from over.

President-elect Trump has stated that his priority in Syria will be to work with Russian President Vladimir Putin to hasten the defeat of ISIS. Any attempt to push Mr. Assad out of power would be deferred. In Jordan, as I learned on a recent trip, many see this approach as more realistic than trying to defeat ISIS while simultaneously expediting Mr. Assad’s ouster. The acute threat posed by ISIS, as well as the al Qaeda affiliate operating in the country, makes such a strategy appealing.

Yet there is also danger in this approach. Mr. Assad has too much blood on his hands to be a stabilizing and legitimate ruler of all of Syria. He is despised by large segments of the Sunni Muslim majority—and for good reason. For five years they have seen their neighborhoods barrel-bombed and shelled, and their fellow countrymen deprived of food, medical care, schools and jobs. The U.S. might defeat ISIS, only to see other extremist groups benefit from the bitterness and disenfranchisement these actions have created. Another wave of jihadism would surely follow, and the war would go on.

Collaborating with Russia to defeat terrorist groups can only work if the U.S. has a vision for what comes afterward. This plan must also be acceptable to Sunni Muslims, Kurds and countries like Turkey, Jordan, Lebanon, Israel, Iraq and the Gulf states. The vision needs to be explained publicly at the same time that any new U.S.-Russian military collaboration is announced. Specifically, Sunni Arabs and Kurds must be promised an alternative to living under the murderous Assad regime. Never again should they have to salute a leader who has committed genocidal acts against their families and neighbors.

To achieve peace, Syria will need self-governance within a number of autonomous zones. One option is a confederal system by which the whole country is divided into such zones. A less desirable but minimally acceptable alternative could be several autonomous zones within an otherwise still-centralized state—similar to how Iraqi Kurdistan has functioned for a quarter-century.

Ideally, Mr. Assad would go. But the prospect of his ouster is not realistic now, given recent battlefield trends and Russia’s role. More plausibly, he could rule an autonomous zone in a new confederation. Less desirably, he could remain president of the country for a time, provided that Sunni and Kurd areas did not have to suffer his direct rule or the presence of his security forces again.

Yet the fall of Aleppo has complicated the situation. Mr. Assad effectively controls the country’s big cities, and he is unlikely to relinquish this power voluntarily. There are two potential paths forward. First, the moderate opposition could be militarily strengthened and assisted to the point where battlefield dynamics shift, and some of the main cities again become contested. But Mr. Trump seems uninterested in such an approach.

A second option is to propose only limited security assistance to moderate groups while literally rebuilding some of the ravaged cities in new locations—the way China has created major metropolitan areas out of nothing—largely for Sunnis and Kurds. Mr. Assad and Russia would be enticed to support this approach with the prospect of an end to the war combined with reconstruction aid. The embattled president would keep the cities he now controls but could be persuaded not to seek to extend his rule further.

This arrangement should be codified by negotiation and upheld in part by international peacekeepers. That force could include Russians in the country’s west, Turks in the north where they are now. Arab, South Asian and European infantry could also contribute. Americans could help with overall command and control, as well as logistics and ongoing counterterrorism operations.

Security in the Sunni Arab and Kurdish autonomous zones would be provided by local police and perhaps paramilitary forces raised, trained and equipped with the direct support of the international community. They would need only limited amounts of heavier arms, making the concept more negotiable with Mr. Assad. Outside powers would agree to stop giving insurgent groups the capacity to attack Damascus or other government-held centers, and would instead channel their security-related aid only to the official and well-supervised local police or constabulary forces.

Foreign assistance for this reconfigured Syrian state should be provided primarily to the autonomous regions themselves. That would enhance the international community’s leverage with the new, regional governments. For Mr. Assad to see any such aid from European, American, and Gulf states flow to the regions that he or his associates controlled, they would not only have to accept autonomy for Sunni Arab and Kurdish zones, but commit to a plan to quickly reduce Mr. Assad’s future role in country’s central governance.

Many Syrians will not like the idea of a confederal nation, or even of a central government controlling half the country with the other half divided into three or four autonomous zones. But such arrangements need not be permanent. The deal could include a provision that calls for a constitutional convention in 10 years to consider whether a stronger central government should be restored.

Many details, such as the borders of future autonomous zones, could be dealt with during a future peace process. But the broad vision should be developed soon. If Mr. Trump joins his plans for Russian collaboration with the creation of a new Syria, he could be the president who finally brought this tragic conflict to an end.

Mr. O’Hanlon, a senior fellow at the Brookings Institution, is the author of “The $650 Billion Bargain: The Case for Modest Growth in America’s Defense Budget,” out earlier this year from Brookings Institution Press.