"As the commander-in-chief, not only does he have a right, he has an obligation to act," Rubio, a Senate Foreign Relations Committee member, said in an interview Friday on ABC News' "Good Morning America" on Friday.
Rubio also affirmed the president's authority to act without seeking the approval of Congress, in contrast to the view of some of his Capitol Hill colleagues.
"The president was authorized to conduct this strike. He's not asking for a declaration of war, he's not committing ground troops over an extended period of time. He was dealing with exigent circumstances," the Florida Republican said. "Obviously, if this is going to be a broader, long-term conflict, it is important that he comes to Congress because we need to pay for it."
Rubio also tied the airstrike against a Syrian government air base to the U.S. fight against terror groups operating in Syria.
Just a week ago -- before Tuesday's chemical attack on a northern Syrian town that killed at least 86 civilians -- the White House said the United States must accept the "political reality" of Syrian President Bashar al-Assad's grip on power.
"I do believe that the administration is shifting in a different direction and rightfully so, and I'm glad to see it," Rubio told "GMA" on Friday. ""I think they understand more fully today than perhaps they did a week ago that as long as Bashar al-Assad is in power, you will not be able to achieve the objective of defeating radical terrorism and radical Islam in Syria."
"As long as Assad is there, you are going to have terrorism emanating from Syria, and that's why he needs to go, in addition to the defeat of those terror groups."
Responding to the chemical weapons attack in Idlib province, the United States on Thursday launched 59 tomahawk missiles against the Shayrat Air Base in Homs Province from which the aircraft carrying the chemical weapons is believed to have taken off.
While strongly defending Trump's swift action, Rubio said the administration is still preparing an overall, longer-term strategy on Syria.
"Ultimately, it has to be, in my opinion, about the removal of Assad and about the defeat of ISIS and al-Qaeda elements," the senator said.
Syrian Foreign Minister Walid Moallem firmly denied that his government was responsible fro the chemical attack. He told reporters at a televised press conference in the capital of Damascus on Thursday that “the Syrian Arab Army has never used chemical weapons and will not use chemical weapons against Syrians and even against terrorists.”
Both Syria and Russia have blamed Syrian rebels for the chemical weapons attack and slammed the United States for its airstrikes.
Rubio used the term "war criminals" to describe Assad and "his patron in Moscow," Russian President Vladimir Putin, a key backer of the Syrian regime.
He said the U.S. airstrike will act as a deterrent to the Syrian leader.
"That is an important airfield," Rubio told "GMA." "It will not degrade his entire capability to do some of this, especially as the Russians continue to support him. But he is certainly not just less capable but, I believe, less willing this morning to do that sort of activity because his cost-benefit analysis just changed dramatically."
ABC News' Conor Finnegan, Benjamin Gittleson, Adam Kelsey, Luis Martinez and Kirit Radia contributed to this report.