He said the ringleader of the attack had been held but he gave no details about his identity or the motive.
It is not disclosed where the attack happened; nor where the bodies are.
The general - a former interior minister who had served at the heart of Col Muammar Gaddafi's regime since the 1969 coup - joined the rebels at the beginning of the Libyan uprising in February.
AnalysisThere are a lot of questions about exactly what happened on Thursday and what the sequence of events was. We're told that Gen Younes had been due to appear before a panel of rebel judges to answer a number of questions on a military matter. We're not entirely sure what that was.
In a conflict like this where there are not many facts and one side of the country is fighting another, we tend to get an awful lot of rumours and suggestions.
For what it's worth, some of the ones we're hearing is that there was a worry among the rebels that the military campaign was not going very well. They wanted to question the general.
Some of the speculation we're hearing in Tripoli, coming from Col Gaddafi's side, is that the general was simply not trusted by the rebels.
Mr Jalil, who heads the rebel National Transitional Council, did not say who the assailants were or where the attack took place.
Although the bodies of Gen Younes and his aides have not been found, Mr Jalil said there would be three days of mourning in their honour.
Gen Younes was due to appear before a panel of judges in the rebel capital, Benghazi.
The exact nature of the questions he was facing is also unclear. Mr Jalil said they regarded military operations.
Some unconfirmed reports said Gen Younes and two aides had been arrested earlier on Thursday near Libya's eastern front.
Shortly after the announcement of their death, gunmen entered the grounds of the hotel in the eastern city of Benghazi where Mr Jalil was speaking, reportedly firing into the air before being convinced to leave.
Ddivisions in Benghazi
Abdel Fattah Younes
- Helped Libyan leader Col Muammar Gaddafi take power in the 1969 coup that ousted King Idris
- Close advisor to the Libyan leader for four decades, rising to the post of general and training Col Gaddafi's special forces
- Appointed interior minister
- Quit the government on 22 February 2011 and defected to the rebels - one of the earliest such moves by a senior official
- Appointed as the opposition's military chief in April, but faced mistrust due to his past ties to Col Gaddafi
The rebels are struggling to break a military deadlock five months into the uprising against Col Gaddafi's rule.
Rebels control most of eastern Libya from their base in Benghazi and the western port city of Misrata, while Col Gaddafi retains much of the west, including the capital, Tripoli.
Late on Thursday AFP news agency reported explosions shaking the centre of Tripoli, as state TV reported that planes were flying over the Libyan capital.
Nato, acting under a UN mandate authorising military action for the protection of civilians, has carried out regular air strikes in the Tripoli area.
Our correspondent says his death will feed international suspicions that the rebel cannot be trusted.
South Africa's ambassador to the UN on Thursday warned that supporters of the rebels were in danger of violating UN sanctions and criticised calls by Western governments for Col Gaddafi to stand down.
The BBC's Barbara Plett at the UN says the growing trend to grant diplomatic recognition to the Libyan rebels is facing opposition on the Security Council.
About 30 countries have recognised the NTC.