Villa: I need to control my temper
Villa, who scored both goals and missed a penalty in the World Cup Group H clash at Ellis Park, tangled with Emilio Izaguirre late in the first half and was lucky to stay on the pitch after striking the Honduran defender.
"It's not something that I am proud of," Villa said in an interview with Spanish broadcaster Canal Plus.
"They're just instincts... in this case I wasn't expecting him to tread on me," he added.
"I was merely standing there and the reaction was to stick my arm out. I'll try in future to keep my cool."
Villa's two goals took his tally for Spain to 40 in 60 matches and he will be leading the line again against Chile in Friday's third and final group match.
A win would put Spain through to the first knockout round, where they are likely to face Brazil or Portugal.