The European champions bounced back from their shock 1-0 defeat to Switzerland in their opening game by dominating the central Americans. [break]
Villa scored a superb individual goal on 17 minutes when he burst between two Honduran defenders and got his second with a deflected shot in the second half.
But the new Barcelona striker wasted an opportunity for a hat-trick when he shaved the post with a penalty awarded after Honduran defender Emilio Izaguirre had clumsily tripped Jesus Navas.
Spain must beat Chile in their last group on Friday to be certain of qualification for the last 16.
Qatar Airways promotes Spain tourism in Kathmandu