In a televison statement, Arroyo commended the military for their actions in responding to the incident and said she was grateful for a peaceful resolution.
She said: "We are preparing proper charges to ensure they will answer for their crimes. The full force of the law will be applied."
Raul Gonzalez, justice secretary, said a special team of prosecutors was already drawing up charges against the officers.
Arroyo said other suspects were at large, and that "we will continue our operations against the rebel soldiers until they are all brought to justice".
A five-hour overnight curfew has been imposed in the capital, beginning at 2400 (1600GMT).
Marga Ortigas, Al Jazeera's correspondent in Manila, described the rebels as a "motley crew" and said the action was less a serious coup than a statement that many people want Arroyo out.
Trillanes, who was elected to the Philippine senate in May, had led the men as they stormed the hotel after they walked out of a court where they had been on trial over a failed coup attempt four years ago.
In July 2003, the soldiers had been among a group of about 300 who had taken over a hotel and mall and demanded Arroyo's resignation.
Having left the court on Thursday, the men then demonstrated on the streets with supporters before marching to the Peninsula hotel.
Calling a news conference shortly after seizing the hotel, one of the soldiers on trial, Brigadier Danilo Lim, a former commander of the elite Scout Rangers unit, had said the group was taking control of the government.
"We make this fateful step of removing Mrs Macapagal Arroyo from the presidency and undertake the formation of a new government," he said.
The men were joined by two Catholic bishops, Antonio Tobias and Julio Labayen, who attacked Arroyo's policies.
Labayen said: "The system has injected massive poverty... we try to fight for justice."
Announcing his decision to come out peacefully, Trillanes said he was ready to face the consequences of his action which he said he had taken for the Philippine people.
"If there is one loser, it is the Philippine nation, because she is still in power," he said, referring to Arroyo.
About 90 minutes earlier troops had stormed the hotel taking an armoured vehicle to batter the door and using tear gas. Some of the soldiers holed up inside were armed with automatic weapons and gunfire was heard.
The tense stand-off was played out live on national television.
|Trillanes was one of a group of soldiers on |
trial for an earlier coup attempt [AFP]
Minutes before the assault, clouds of tear gas were seen in the hotel lobby.
Hotel guests were evacuated before the troops went in, but several journalists remained inside, despite warnings from government authorities to leave for their own safety.
Reports said at least two people were injured in the assault on the hotel, but there have been no reports of any other casualties.
Earlier, as the standoff played out, Trillanes had been defiant saying: "One thing I can assure you is we have more than enough willpower, fighting spirit to bring this government down."
He had been joined in the hotel by other dissident officers and leaders from the opposition.
Arroyo has faced growing opposition to her rule from various sectors of Philippine society, but during seven turbulent years in power she has survived at least three coup attempts and three efforts to impeach her.