However, it says land and maritime borders will remain closed.
Several people were killed when gunmen attacked an Ivorian army checkpoint in the border town of Noe. Ministers said the gunmen had crossed from Ghana.
Ivory Coast has blamed previous attacks on supporters of ousted President Laurent Gbagbo hiding in Ghana.
“After 48 hours of observation of the movements of people and goods between the two countries, it is decided that only the air borders will be opened from Monday,” a statement from the office of President Alassane Ouattara said.
The statement, broadcast on state TV, said Ivorian airspace would reopen to Ghanaian flights from midnight.
In August, Ivory Coast officials blamed Gbagbo loyalists based in Ghana for attacks in the commercial capital Abidjan that killed 10 soldiers.
Ivory Coast is recovering from months of unrest following a disputed election.
Mr Gbagbo refused to accept his defeat to President Ouattara, who eventually ousted his rival with the help of former rebel forces, the UN and former colonial power France.
The former president is currently in The Hague, awaiting trial at the International Criminal Court on charges of crimes against humanity.