That put the zone effectively under Syrian regime control as the remaining strip of territory was within weapons range.
Bashar al Assad's regime, backed in the war by Russia and Iran, is seeking to crush the last major rebel enclave near Damascus in a ferocious campaign that the war monitor Syrian Observatory for Human Rights (SOHR) says has killed 893 civilians in the last 18 days, including 91 on Wednesday.
The pro-regime commander, who spoke on condition of anonymity because he was not authorised to talk to the media, confirmed a report by the Britain-based Observatory late on Wednesday that the enclave had effectively been sliced in two.
But Wael Alwan, the Turkey-based spokesperson for Failaq al Rahman, one of the main rebel groups in eastern Ghouta, denied that the territory had been cut in half.
"No" he said in a text message when asked if the report was correct.
Red Cross says aid delayed
Meanwhile, an aid convoy that intended to go to eastern Ghouta later on Thursday was postponed, the International Committee of the Red Cross (ICRC) said.
Ingy Sedky, the ICRC spokesperson in Syria, said Thursday's "convoy is postponed. No confirmation yet on when it will take place."
Sedky added that "the situation is evolving rapidly on the ground, which doesn't allow us to carry out the operation in such conditions."
Earlier this week, the first convoy in weeks made it into eastern Ghouta, but 14 of the 46 trucks were not able to fully offload critical humanitarian supplies because of stepped-up violence.
The United Nations says 400,000 people are trapped in the towns and villages of eastern Ghouta.
They have been under regime siege for years and were already running out of food and medicine before the assault. Many civilians have fled from the front lines into Douma, a town in the enclave.