From the former residence of Aslan Abashidze, who fled Ajaria on Wednesday after running it as a personal fiefdom for more than a decade, Saakashvili praised those whose defiant mass protests had helped bring down Abashidze.
The rebel leader is now in exile in Moscow, a source in his entourage said.
"I'd like to say thank you to all of you, for your bravery," Saakashvili said in a brief speech on Thursday. "Thank you for everything you did."
Celebrations erupted in Ajaria's main town Batumi after Abashidze left the region, following talks with Russia's former foreign minister Igor Ivanov.
Saakashvili, elected in January after leading a bloodless revolution to oust veteran leader Eduard Shevardnadze last year, has vowed to bring Ajaria and other unruly regions of the former Soviet republic back under central control.
"I congratulate everyone on this victory, on the beginning of Georgia's unification. Georgia will be united," he said in Tbilisi before flying to Batumi.
In an interview soon after his arrival in Batumi, Saakashvili said Abashidze had been "some kind of mini-Saddam Hussein".
"But people went out and people destroyed him, and that's the force of democracy," he added.
"Georgia has two peaceful revolutions within the last months without any bloodshed. This is a very unique chance."
"...people went out and people destroyed him, and that's the force of democracy"
Bringing back to the central government fold two other regions - Abkhazia and South Ossetia - is likely to prove much more difficult.
Ajaria, whose residents are ethnic Georgians, had only sought autonomy. The other areas have different ethnic compositions and declared full independence a decade or more ago after wars costing thousands of lives.
Abashidze had in recent weeks ignored calls for his resignation and imposed a state of emergency. He spent Wednesday evening in talks with Ivanov, who launched his mission after months of confrontation threatened to spill over into bloodshed.
Later, Abashidze and Ivanov slipped quietly away from the rebel leader's residence in the Ajarian capital Batumi.
Russia is a major player in the region, with a military base and a keen interest in oil transit routes.