The group has remained firmly opposed to Syrian President Bashar al-Assad and to the Islamic State jihadist group.
A senior member of Jaish al-Islam said planes had targeted a "secret meeting" of commanders, confirming Alloush was among those killed.
Syria's regime claimed responsibility for his death, which was seen as dealing a heavy blow to the nearly five-year uprising and also complicating the fragile peace process.
UN special envoy Staffan de Mistura's office said he has "intensified efforts" to convene talks on January 25, hopefully including the "broadest possible spectrum" of opposition representatives.
He "counts on full cooperation of all the relevant Syrian parties in this process," the statement said, adding: "Continuing developments on the ground should not be allowed to derail it."
The talks are the first step of an ambitious 18-month plan endorsed by the UN Security Council to end Syria's war, which has killed more than 250,000 people.
- 'Severe blow' to peace talks -
But analysts feared Alloush's death would thwart the already-fragile negotiation process.
Backed by Saudi Arabia, Jaish al-Islam was one of the most influential armed groups invited to broad-based opposition talks in Riyadh earlier this month.
Representatives in Riyadh agreed to eventual negotiations with the regime and were set to choose at least part of the opposition delegation for the talks.
Analyst Karim Bitar said Alloush's death is "a severe blow to the Riyadh negotiations process".
"Given Alloush's authoritarian temper and strong rule, it will take time for Jaish al-Islam to recover from this blow and for the alternative leadership to emerge," he said.
Aron Lund, editor of the Carnegie Endowment's Syria in Crisis website, said: "Those negotiations needed hardliners like Zahran Alloush to be involved for their credibility."
Alloush was a "rare successful centraliser in the Syrian rebel movement," Lund added, and with him gone, opposition cohesion could "unravel."
Abu Hammam al-Buwaydani was elected to replace Alloush just hours after his death, according to the Syrian Observatory for Human Rights.
A 40-year-old businessman and fighter from Douma in Eastern Ghouta, he hails from a family with strong ties to the Muslim Brotherhood, the monitor said.
In his first video address, published Saturday, a solemn Buwaydani said the difficulties faced by Jaish al-Islam "have only made us fiercer."
He urged rebels to be "one cohesive rank" in the fight against the regime, stressing his group's "moderate approach".
- IS loses strategic dam -
Alloush's death also appeared to halt the planned evacuation of some 4,000 people, half of them jihadists, from Damascus' southern districts Saturday.
The plan was to see the evacuees transferred out of Qadam, Hajar al-Aswad and the besieged Palestinian camp of Yarmuk into northern Syria, according to a government official.
Those moved are expected to include members of the Islamic State (IS) group and Al-Qaeda-affiliated Al-Nusra Front.
But a security source close to the negotiations told AFP the plan was now on hold.
"Jaish al-Islam was supposed to provide safe passage through areas east of Damascus for the buses heading to Raqa," IS's Syria bastion, the source said by telephone.
"About 1,200 people were supposed to leave today (Saturday), but the death of Zahran Alloush means we are back to square one," he said.
He said buses standing by to transfer the evacuees had left empty and "the plan was on hold until Jaish al-Islam reorganises itself".
The deal came after two months of intense talks between government and district leaders, he said.
Syria's conflict erupted in 2011 with anti-government protests but has spiralled into a multi-sided civil war.
In northern Syria Saturday, a coalition of Kurdish and Arab groups seized the key Tishreen Dam on the Euphrates and seven villages on the river's eastern bank from IS.
Syrian Democratic Forces spokesman Talal Sello told AFP dozens of IS fighters had been killed.
The SDF can now cross into IS-controlled territory along the river's western bank, bringing it less than 30 kilometres (20 miles) from Manbij, an IS stronghold.