"We abstained because we felt the resolution was unbalanced, it only targeted the Syrian government," Deputy International Relations Minister Ebrahim Ebrahim said on Friday.
"It said nothing about the opposition who are now fighting in the capital."
The rebel forces in Syria were not just defending themselves, but were on the offensive and wanted to take power, he added.
On Thursday, Russia and China vetoed a security council resolution to extend a UN observer mission in Syria for 45 days. The resolution also threatened Syrian authorities with sanctions if they did not stop using heavy weapons against the uprising and withdraw troops from towns and cities.
The vetoed resolution received 11 votes in favour. South Africa and Pakistan abstained from voting at UN headquarters in New York.
Ebrahim said South Africa supported the extension of the deadline for the UN mission in Syria, but the resolution should not have extended this to include sanctions.
The Russians were against this aspect of the resolution too, as they said it could open the door to military intervention.
South Africa was not necessarily against sanctions as it supported "stern action" as called for by Kofi Annan, the Joint Special Envoy to Syria of the UN, and the League of Arab States.
Ebrahim said South Africa had made recommendations to balance the text of the resolution to include measures against the opposition in Syria for non-compliance with Annan's plan.
"These proposals were rejected by the drafters of the resolution, leaving South Africa no option but to abstain in the vote."
Ebrahim said it was not just a question of language.
"Our view is that a one-sided resolution would only make the situation on the ground worse, pushing the government to further pursue the military option and emboldening the opposition to continue to reject talks … In a complex, divided society such as Syria, there can be no military solution."
South Africa was calling for a Syrian-led solution through a negotiated settlement.
"The question is whether they do so now or after a bloody and protracted civil war," he said.
Ebrahim said the outcome of the vote reflected the deep divisions and narrow interests among the five permanent members of the security council.
South Africa is a non-permanent member of the 15-nation council.
There are now two competing resolutions before the council to extend the mandate of the UN Supervision Mission in Syria. Its mandate ends on Friday.
"We hope the Security Council will be able to rise above its deep divisions and adopt the extension unanimously."
Ebrahim said South Africa was wary of resolutions that could lead the way to military intervention, following events in Libya last year. South Africa supported a UN resolution on Libya, but felt members went beyond the terms of the resolution in enforcing a no-fly zone.
"Because of our experience with the Libyan resolution we are very cautious as to how we take future resolutions," he said.
According to a UN communiqué on Syria the crisis between the government and opposition movement had "continued unabated" since an uprising against president Bashar al-Assad began about 16 months ago.
The UN estimated that over 10 000 people, mostly civilians, had been killed there, and tens of thousands displaced.
The six-point plan that Annan proposed, and hoped Syria would accept, includes that they commit to work with the envoy, that they stop the fighting, stop troop movements in populated areas, start pulling troops out of these areas, allow freedom of movement in the country for journalists, and respect the people's right to demonstrate peacefully.
It also calls for the release of arbitrarily detained prisoners, a list of where they are, and for humanitarian assistance. &ndash Sapa