Hillary Clinton said it was "wholly unjustified" and urged Syria to protect diplomatic staff.
Veteran politician Hassan Abdul Azim said about 100 protesters tried to get into his office as Mr Ford arrived and then surrounded it, trapping them both.
US officials said the mob was violent and seriously damaged embassy vehicles, but that Mr Ford was unharmed.
Ms Clinton said the attack was "unwarranted" and condemned it "in the strongest possible terms".
She praised Mr Ford's "admirable courage" as a "vital advocate for the legitimate aspirations" of the Syrian people.
She encouraged the US Senate to confirm Mr Ford - who was named ambassador last year during recess to avoid Republican opposition - so he could "continue his critical and courageous work".
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