Bernardo Alvarez's ouster follows remarks by Venezuelan President Hugo Chavez about breaking off ties with the US over Caracas' refusal to welcome Larry Palmer as ambassador there.
On Wednesday, State Department spokesman Mark Toner said the US regretted Chavez's stance on Washington's would-be ambassador, but did not say whether Alvarez would be asked to leave.
"We did say that we regret, obviously, the Venezuelan government's decision to withdraw agreement for ambassador designate Palmer," he told reporters. "It affects our ability to carry out normal diplomatic relations, and we also said that there could be consequences for that action with that."