General Abdel Fattah Al-Burhan, who heads Sudan's ruling sovereign council, met Netanyahu for previously unannounced talks in Entebbe on Monday that appeared to signal an end to Sudan's long-standing boycott of Israel.
Soon after their meeting, Netanyahu announced that the two leaders had agreed to cooperate towards normalising ties.
Read more: Sudan's rapprochement with Israel exposes weakness of democratic transition
Sudanese military spokesman Amer Mohamed al-Hassan told Al-Jazeera on Wednesday that there was an agreement "in principle" for commercial aircraft travelling from South America to Israel to use Sudan's airspace.
He said that technical aspects of the overflights were being studied and Sudan had not agreed to flights by Israel's national carrier El Al.
Netanyahu has previously expressed interest in opening Sudanese airspace as it would cut hours off flight times from Israel to South America, the fourth most popular destination for Israelis.
Read more: Power and politics: Israel makes new inroads into Africa
In 2018, Israel renewed long-severed ties with Chad, who together with Egypt and Sudan form an African air corridor for flights.
"With Sudan we are now establishing cooperative relations," Netanyahu said in a campaign speech on Wednesday. "We will overfly Sudan."
Sudan has long been part of a decades-old Arab boycott of Israel over its treatment of Palestinians and its occupation of Arab lands.
In the wake of the Six-Day War of 1967 in which Israel occupied the Palestinian territories and seized the Golan Heights from Syria, Arab leaders held a historic meeting in Khartoum to announce what became known as the 'three nos' - no peace, no recognition, no negotiations with Israel.
Agencies contributed to this report.