More than 700 people packed inside including actors Benedict Cumberbatch and Robert Lindsay, who had both played the king.
The king's remains had been found under a council car park in 2012.
Her majesty the Queen praised the reburial and said it was a moment of "great national significance".
In the order of service, she said: "Today, we recognise a king who lived through turbulent times and whose Christian faith sustained him in life and death."
Richard III was killed in battle at the age of 32 in August 1485.
During the service the Archbishop of Canterbury, Most Revd Justin Welby said: "Whether we bear a white or a red rose, whether for Richard or Henry, whether for Stanley or Howard, whether for Leicester or York, we recognise at the graveside that all our journeys lead us to this place where reputation counts for nothing and all human striving falls to dust.
As the king's coffin was lowered into the cathedral grounds Archbishop Justin said "Earth to earth, ashes to ashes, dust to dust".
The Bishop of Leicester, the Rt Rev Tim Stevens, gave the sermon: "Whether we are Ricardians or Shakespeareans, whether we see through the eyes of Olivier, McKellen or Cumberbatch, whether we recognise a warrior or a scholarly pious thinker, today we come to accord this King, this child of God, and these mortal remains, the dignity and honour denied them in death."
He added: "Five hundred years after the Wars of the Roses we still face the risk of damaging tribal behaviours, of the destructive instincts which can so quickly turn neighbours into strangers and corrode our sense of the common good."