His comments echo those of outgoing European Command chief Adm. James Stavridis, who predicted that Syria will "break apart entirely" once rebel forces topple longtime president Bashar Assad.
The war has increasingly turned to a stalemate, as government troops loyal to Assad batter rebel forces with air power, heavy artillery and possibly chemical weapons, according to U.S. intelligence reports.
But Assad has also carved out significant support among the country's ruling Alawite population, a strain of Shiite Islam the Assad family practices, in western Syria.
When Assad falls, Middle East watchers fear it could invite a prolonged civil war as Sunnis and Alawites square off to fill the power vacuum in the country, mirroring the bloodshed seen in post-Saddam Hussein Iraq.
The Pentagon chief noted Washington was committed to the "full range of tools" available to end the violence in Syria and "helping the Syrian people transition to a post-Assad authority."
"This will help restore stability, peace, and hope for all Syrian people," Hagel said. "That goal is shared by our allies in the region, not only those bordering Syria, but also our partners in the Gulf."
That said, Hagel made no direct mention of possible military action by U.S forces, including arming rebel forces, targeting Assad's air defenses or setting up a no-fly zone with American warplanes, during the speech.
"The United States will remain engaged in helping shape the new order, but we must engage wisely," Hagel said.
"This will require a clear understanding of our national interests, our limitations, and an appreciation for the complexities of this unpredictable, contradictory, yet hopeful region of the world," he added.
But since reports the Assad regime has used chemical weapons, crossing a "red line" set by President Obama, has fueled congressional calls for U.S. action.
A bipartisan group of four senators on Thursday went to the Senate floor to pressure Obama to take more aggressive actions with Syria.
Sens. John McCain (R-Ariz.), Carl Levin (D-Mich.), Lindsey Graham (R-S.C.) and Bob Menendez (D-N.J.) all said Obama should put military pressure on the Syrian regime by arming rebel groups or launching air strikes against the country's defenses.
Levin, the chairman of the Senate Armed Services Committee, said it was “essential” that the U.S. “step up the military pressure on the Assad regime.”
But U.S. forces are already "very involved" in providing non-lethal support to the rebels, and assisting neighboring countries like Jordan and Turkey in preventing the war from spilling over Syria's borders, according to Hagel.
"Hundreds of DoD personnel are working alongside their Jordanian counterparts to enhance Jordan’s border security" and track the chemical weapons threat from Assad, Hagel said.
"We have given non-lethal assistance to the Syrian opposition, including the armed opposition, and that support is growing," he added. "The U.S. military has been very involved in delivering those supplies."
So far, over $500 million in humanitarian aid alone has been spent by Washington, to help deal with the thousands of war refugees streaming out of Syria, according to the Pentagon chief.
While the war drums in Congress have begun to beat louder in recent weeks, Hagel pushed back against calls from Capitol Hill for military action.
"A common thread woven into the Middle East fabric is that the most enduring and effective solutions to the challenges facing the region are political, not military," he said.
America’s role in Syria and the region writ large "is to continue to help influence and shape the course of events [through] diplomatic, economic, humanitarian, intelligence, and security tools," Hagel added.
--updated at 10:16pm