Jonathan spoke shortly after he was decorated as the National Grand Patron of the Boys Brigade of Nigeria at the Aso Villa Chapel, Abuja.
The President said he was particularly happy because the information at his disposal was that Ekiti State would erupt in crisis at the end of the governorship election.
He commended the Nigeria Police and other security agencies for ensuring that peace reigns.
He said the Ekiti victory and the victory by the Super Eagles were indications that Nigeria would soon take its rightful place among the comity of nations.
Jonathan said, "I am particularly happy today because of the two events that happened on Saturday. Others have made reference to that . One was the election in Ekiti State.
"I am quite happy not necessarily that my party, the PDP won. Yes, as the leader of the party, I must be happy, but it is beyond that,
"I was told that there may be crisis in Ekiti, because the report I got before the election the feeling is that yes, one party might win or lose, but there will be fire and brimstone. I have to commend the Nigerian Police and other security agencies.
"And today Ekiti is in a peaceful state. Elections are over and of course to cap it all, those of you who watched the late night match the Eagles made us proud.
"I only see this as a sign of unfolding of a greater nation coming. Nigeria will surely take its rightful place in the comity of nations. All the challenges will surely pass away."
The President commended Nigerians for their prayers which he said had so far sustained the country.
He identified the activities of the Boko Haram sect as one of the obstacles facing the country, adding that good will always overcome evil.
He said, "Let me use this unique opportunity to appreciate all Nigerians within this period because those of us who are from the Eastern region knew what the civil war was.
"But since after that time, this country had not passed through this stress. I appreciate the feelings of Nigerians, the endurance, I also appreciate the support you are giving to the government.
"Let me specially appreciate those of you who are prayer warriors, who have been praying day and night for God to intervene.
"I always believe that any journey to where is good passes through some bumps. The Boko Haram is one of those obstacles but my conviction is that good will always overcome evil.
"In human history, no matter the challenges, good will always prevail. No matter how dark the night is, light will always come. Continue to pray for this country, surely, the light will come."
The first lesson of the service was read by the President's wife, Patience, from Exodus 3: 1-12, while the Deputy Speaker of the House of Representatives, Ike Ekweremadu, read the second lesson from Matthew 25:14-30.
The service was attended by the embattled Deputy Governor of Adamawa State, Bala Ngilari; members of the Federal Executive Council and other top government officials.
Thanks
