The bombing was described as "frenzied".
The deal for the city of Daraa is the latest in a string of such agreements the government has used to retake large parts of the country. Only one ambulance was able to get to the town and civilians relied on their cars to bring out at least 150 wounded.
A Syrian war monitor and rebels on Sunday said jets bombed an opposition held town in Quenitra province in the first such aerial strike in a year.
The deal will see the entire Quneitra province near the Israeli-occupied Golan Heights back under the government control.
Earlier on Tuesday, at least 10 civilians were killed when a suspected Russian airstrike hit a school that serves as a shelter in the village of Ain el-Tineh in Quneitra countryside, about 7 kilometers (4 miles) from the Israeli frontier, according to a Syrian search and rescue team.
Israel has occupied the Golan Heights since 1967, and a cease-fire deal was reached in 1974.
The radical organizations, including the al-Nusra Front, the Free Syrian Army and other factions, chose to cease the armed struggle in Quneitra by virtue of an agreement signed with the government of this Arab country.
For Israel, the medical aid program can help win hearts and minds in border areas where the number of refugees has increased in recent weeks as Syrian President Bashar al-Assad's forces advance in an offensive to recover southwest Syria.
Rebels had agreed to a "reconciliation" deal with the government on Wednesday under which they would give up the hills around the city and surrender heavy weaponry, a statement from Nawa's negotiation delegation said.
Syrian and Russian bombardment battered the province of Quneitra, which remains mostly in rebel hands, for a second day on Monday.
Their terms also typically include the mass transfer of thousands of rebels and civilians to opposition-held Idlib, in what rights groups and activists say may amount to forced displacement. But the talks faltered, triggering the overnight onslaught. Jordan has said it will not open its borders to the newly displaced Syrians.
The Observatory said warplanes and ground forces have also targeted with a barrage of missiles the southern tip of the region, which is held by a militant group affiliated with the Islamic State group.
A brutal crackdown paved the way for a full-fledged conflict that has since killed more than 350,000 people and displaced millions.
The marchers waved white flags at Israeli soldiers as they walked toward the frontier in the Golan Heights, demanding protection from the relentless airstrikes, before they turned back.
Syrian regime forces backed by Russian Federation made sweeping advances on Monday against rebels holding out in the country's south, a monitor and state media said.
The Times reported that United States national security adviser, John Bolton appeared to corroborate a tit-for-tat deal, quoting him as saying that "There are possibilities for doing a larger negotiation on helping to get Iranian forces out of Syria. which would be a significant step forward".
A negotiated deal to evacuate Foua and Kfraya villagers earlier this year faltered after the evacuation of only 40 people from a third village.