Xanana Gusmao, the prime minister, who was attacked an hour later, escaped unhurt.
"I'm happy to be back in Timor-Leste," Ramos-Horta told a news conference at the airport.
But he quickly urged the new commander of the rebel soldiers to surrender, saying he had lost patience with the army rebels.
|Thousands welcomed the president|
with flags and cheers [Reuters]
"I ask Gastao Salsinha not to keep staying in the jungle but to surrender soon to the church or the state authorities and face justice," he said.
"I don't want anybody to die," he said, holding back his tears. "Gastao should surrender to justice and hand over his weapons."
Salsinha took over as rebel chief after Reinado was killed during the assassination attempt.
Al Jazeera's Paul Allen, reporting from Dili, said Ramos-Horta, who was emotional at times, decided to issue a warrant of arrest against Salsinha, admitting he may have been naïve to think he could talk the rebels into coming down from the mountains.
He also said investigations showed the rebels may have had assistance from individuals within Indonesia.
"The ongoing investigation shows a lot of contacts that Mr Alfredo Reinado had with elements in Indonesia and I repeat - elements in Indonesia. In no way it implicates Indonesian government," Ramos-Horta said.
The president added that his Indonesian counterpart, Susilo Bambang Yudhoyono, had assured him that the government would look into any evidence to see if individuals in the country had any part in aiding the rebels.
But the rebels are blaming presidential guards for firing first.
Al Jazeera was handed a tape where Reinado's men said they had no intention of attacking the president.
"If we are going to attack the president, how come we go with two vehicles and several men? It's impossible.
"We came there, and we parked in front of the gate, and we came inside and then suddenly they shoot at us. We had not come to fight, we'd come to talk with the president," a rebel said on the tape.
Returning from more than two months of medical treatment in Australia following the assassination attempt in February, Ramos-Horta was greeted by thousands of people shouting "Viva President Ramos-Horta".
Huge posters saying "Mr President, Timor is praying and waiting for you" dotted the route to his house near a tourist beach in the eastern part of Dili.
He was received by Gusmao, Mari Alkatiri, the opposition leader, and other government ministers and diplomats.