Josep Borrell told journalists the breakthrough deal signed by Ethiopia's government and Tigrayan rebels to end the war in the north of the country is "good news."
But, "Making peace is much more difficult than making war," he said.
But the two sides now "have to reach a permanent ceasefire", Borrell said, something that was "not going to be easy."
Indeed, on Friday Tigrayan authorities accused Ethiopia's government of carrying out a drone strike on civilians, less than 48 hours after the warring parties signed a deal to end their bloody conflict.
The rebel Tigray People's Liberation Front (TPLF) also alleged that Prime Minister Abiy Ahmed's government had carried out attacks against civilians in the Tigrayan city of Maychew on Thursday.
"According to sources at Lemlem-Karl Hospital, drone of #Ethiopia has attacked civilians," Kindeya Gebrehiwot said on Twitter.
AFP has not been able to independently verify the allegations.
Additionally, There was no immediate response from Ethiopian government officials or the African Union (AU) to requests from AFP.
The African Union sponsored the South Africa talks between Addis Ababa and Mekele, the main Tigrayan city.
While welcoming the Pretoria agreement reached on Wednesday, Borrell said the international community should also remember the "tens of thousands, some figures say more than 100,000, of people who have been killed and those whose have been victims of the worst atrocities" in the conflict.
The peace deal was reached less than 48 hours before the second anniversary of the outbreak of the conflict, after nine days of negotiations in Pretoria mediated by the African Union.
The European Union stands "ready to support the African Union in their efforts for peace, reconciliation and recovery" in the country, he added.
The G7 foreign ministers' meeting in Germany, which began on Thursday, has so far been dominated by the war in Ukraine.
But on the second and final day of their discussions, the ministers are also due to discuss recent unrest in Iran and relations with Africa.