And at least 45 rebels were killed when they tried to break an army siege in the central city of Homs.
Observatory director Rami Abdel Rahman said the rebels had launched an attack late Wednesday near the Khaldiya neighbourhood, controlled by the army, when they were ambushed.
The violence comes nearly a week after rebels launched an all-out attack on ISIL, and almost three years into a war that erupted after Assad cracked down brutally on a peaceful pro-democracy movement.
Jihadists were initially welcomed by Syria's rebels, but ISIL became hated because of its systematic abuses and its bid to dominate areas lost to the regime.
In a counterattack, ISIL launched car bomb assaults late Wednesday against rival rebel checkpoints, the Observatory said.
"At least nine people were killed in a car bomb attack by ISIL on a rebel checkpoint... in Al-Bab town" in Aleppo province, Abdel Rahman told AFP.
There were similar attacks in Hreitan and Jarabulus in Aleppo, and in Mayadeen in the eastern province of Deir Ezzor.
The attacks came after rebels overran ISIL's Aleppo headquarters on Wednesday, as claims emerged that the group had massacred prisoners there.
In Raqa, the only provincial capital lost by the regime, fighting raged near the governorate building, which ISIL has used as its headquarters for several months.
While rebels in Raqa appeared to be advancing, ISIL was fighting back in the countryside, especially in the border town of Tal Abyad, from which they were expelled earlier this week.
ISIL is believed to be holding hundreds of activists, rival rebels and foreigners, including journalists, at bases in Raqa province.
Activists say Raqa has become "a city of ghosts", with bodies in the streets and people afraid to leave their houses because of the violence.
Huge car bomb in Hama
The fighting has not stopped the main war with the regime.
At least 18 people, among them women and children, were killed in the huge car bombing in Kafat in central Hama province on Thursday, the Observatory said.
Much of the province, including Kafat, is still under regime control, and state television reported the "terrorist" blast, saying 16 people were dead and tens more wounded.
In Aleppo, warplanes carried out a new air strike on the rebel-held district of Sheikh Maqsud.
A brutal aerial offensive by the regime against Aleppo that started on December 15 has killed hundreds, mostly civilians.
In southern Damascus, troops fired rockets at Yarmuk, a Palestinian refugee camp that has been under siege for a year, the Observatory said.
Some 20,000 of its pre-war population of 170,000 are trapped with little food and medicine, and reports say 15 people have died from hunger there since September.
On Thursday, the spokesman for the UN agency for Palestinian refugees UNRWA described "profound civilian suffering" in the camp.
Chris Gunness said there was "widespread malnutrition" and reports of women dying in childbirth for lack of medical aid.
He urged the regime and other parties to allow aid into the camp, which is controlled by rebels and under a tight Syrian army siege.
But state television said an aid convoy carrying 5,000 food parcels had been blocked from entering Yarmuk by "terrorist gangs" who opened fire.
The violence comes less than two weeks away from a slated peace conference in Switzerland.
The fractious opposition National Coalition has postponed a final decision on whether to attend the January 22 talks, but members said Thursday they face international pressure to participate.
"There have been clear signs indicating the Coalition must go to Geneva," said Coalition member Samir Nashar.
But he warned that the Coalition's legitimacy was at stake, amid widespread opposition towards the talks.
"The entire revolutionary movement in Syria is against Geneva," he told AFP.
Iranian President Hassan Rouhani said the peace talks would fail if Tehran, a close Assad ally, does not participate.