Tunisia and South Africa filled the final two places for the round of 16 after a tense finish to the group stage in Egypt.
Sixteen people, including three children, were killed outside the Mahamasina stadium during national independence day celebrations.
Resistance to vaccination against the infectious disease and malnutrition are seen as the major contributors towards the largest measles outbreak in the island nation's history.
In the run-off vote on December 19, Andry Rajoelina took 55.7 percent and Marc Ravalomanana won 44.3 percent, according to the final results.
Former president Andry Rajoelina received more than 55 percent of the vote while his opponent Marc Ravalomanana received more than 44 percent according to provisional results.
Voters headed to the polls for the second round in a run-off between two former heads of state who have had a long standing political rivalry.
Madagascar hopes for a second peaceful election since upheaval in 2009, when former president Marc Ravalomanana was forced out of office by protests led by Andry Rajoelina in what the AU and other international organisations said was a coup.
Andry Rajoelina and Marc Ravalomanana both failed to secure 50 percent of the vote required for a first-round win and the run-off scheduled for December 19.
Madagascar's presidential candidate Antry Rajoelina was ahead with 40.9 percent of the votes against 36 percent for rival candidate Marc Ravalomanana, preliminary results show.
Counting of votes from a presidential poll underway with former president Andry Rajoelina commanding a slim lead in early results published by the electoral commission.
Voters in Madagascar voted to elect a president with hopes that a new leader will take their country out of chronic poverty and corruption. The 36 candidates have all promised to improve the country's economy.
The Indian Ocean’s vanilla island is set for its presidential election on November 7, with 36 candidates on the ballot. Two could advance to a possible run-off on December 19.
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