Baroness Amos said she was sad that a three-day ceasefire to allow aid into the old part of Homs had been broken.
The events were “a stark reminder of the dangers that civilians and aid workers face every day across Syria”.
She said the UN would do “the best we can” but needed “safety guarantees”.
The convoy came under attack from mortars and gunfire as it was leaving Homs on Saturday, the second day of the humanitarian ceasefire.
Syrian authorities have blamed the attack on rebels, but they in turn say that President Bashar al-Assad’s forces were responsible for the incident and for earlier mortar fire that delayed the start of the operation on Saturday morning.
“Am deeply disappointed [the] humanitarian pause was broken today in Old Homs,” Baroness Amos said on her Twitter page.
She said that the aid workers had been deliberately targeted and that she commended their courage.
“The UN [and its] humanitarian partners won’t be deterred from doing our best to bring critical aid to people but we need safety guarantees for aid convoys.
“I continue to call on those engaged in this brutal conflict to respect the humanitarian pause, ensure the protection of civilians and facilitate the safe delivery of aid.”.
The Syrian Arab Red Crescent said that one of its drivers was injured when mortars landed close to their convoy and shots were fired at their trucks.
Seven Red Crescent workers and a similar-sized UN team were “pinned down” in the Old City area of Homs for several hours.
The Syrian Red Crescent’s Khaled Erksoussi said the group took refuge in “buildings and safe areas” until they were able to get out, shortly before 22:00 local time (20:00 GMT). They had to leave two of their damaged trucks behind.
The Red Crescent, in a joint operation with the UN, is trying to deliver food, water and medicine by truck to some 3,000 civilians in rebel-held areas.
“Although the team was shelled and fired upon we managed to deliver 250 food parcels, 190 hygiene kits and chronic diseases medicines,” it said on Twitter.
On Friday, the first day of the agreed three-day ceasefire, more than 80 children, women and elderly people were evacuated.
Many of those evacuated looked frail and described extreme hardships inside the area, which has been under army siege for nearly a year-and-a-half.
They said bread had not been available for months, and many residents were gathering weeds and leaves to eat. Many people were left behind who wanted to leave, they said.
Relief officials had earlier said the plan to send supplies into the embattled area was extremely sensitive, given the reluctance by some on the government side to see supplies going into rebel-held areas.
A second group of civilians is due to be evacuated from the city on Sunday. But a Red Crescent spokesman told the BBC that guarantees were needed for the humanitarian operation to continue.
Homs has been a key battleground in the uprising against President Assad.
The army launched a series of big attacks to recapture rebel areas in the Old City in the beginning of 2012, with almost daily bombardments.
Thousands have been killed, large areas have been reduced to rubble and many neighbourhoods lie in ruins.
Another round of talks is scheduled to begin on Monday and the Syrian government has confirmed it will attend.