"The bloodletting has to stop. We are going to make sure it stops," he said in a national address.
His call came as the northern state of Sokoto began implementing the Islamic legal code, or Sharia.
Sokoto is the second Nigerian state to formally adopt Sharia, after neighbouring Zamfara did so in January this year.
United Nations Secretary-General Kofi Annan hailed the anniversary as "a significant landmark in Africa's quest for political stability and economic progress". President's promise
During his address, President Obasanjo pledged that his government would work harder to ensure progress for all Nigerians.
He said Nigeria's image in the world had been improved.
"By all indications, we can now proudly claim to have been accepted by the international community," he said.
"We have taken our rightful place among the comity of nations. We now enjoy the confidence of our development partners and major international organisations, such as the World Bank and IMF," he added.
President Obasanjo promised to continue his fight against corruption.
He noted that his government had recovered 100bn naira ($1bn) of stolen cash and assets while another $2bn had been frozen in foreign accounts, "with the possibility of recovery and repatriation," he said.
Nigeria united
He also dismissed any fears of the country disintegrating into separate states.
"I don't see any sign of breaking up in Nigeria," President Obasanjo told reporters.
"And maybe because we had a civil war virtually based on ethnic grounds, people see any flareup in Nigeria, no matter if it is between two schoolchildren, as likely to lead to Nigeria's break-up," he added.
In a conciliatory move towards those who fought in the secessionist Biafran army in the late 1960s, the president announced that soldiers who were dismissed from the army for fighting on the Biafran side would now have their dismissals commuted to retirement.
"(It) is another step to put the unsavoury past behind us and there may be more of such acts of reconciliation in the future," he said.
The BBC's Lagos correspondent says that the president is generally perceived as a sincere man working in the national interest, but the upsurge of violence has led many Nigerians to question the basic terms under which they should remain united.
No ceremony
Sharia was introduced in Sokoto without formal ceremony which accompanied its introduction in Zamfara, in order to avoid controversy.
Governor Attahiru Bafawara appointed 43 "Alkalis" or Islamic
judges to preside over 35 Sharia courts in the state, according to local media reports.
Sharia law includes punishments such as the amputation of the limbs of those convicted of theft or robbery and the stoning of women caught in adultery.
As in Zamfara, Christians will not be affected by Sharia but many Christians are bound to perceive the implementation of Sharia as a threat to their way of life.
Plans to introduce Sharia in Kaduna, another northern state, resulted in violent clashes in the state capital between Christian and Muslima in February this year which left hundreds dead.
The fighting erupted again last Monday and hundreds more people were killed.
Governors of the mainly-Muslim northern states had agreed with the federal government in February to suspend any implementation of Sharia.
But the authorities in Sokoto, which is the historic centre of Islam in Nigeria, say they had already announced the move and could not go back on the pledge.