Barcelona's new £34m striker could even afford to spurn the chance of a richly-deserved hat-trick, shocking a 55,000 crowd with a second-half penalty miss as the European Champions threatened to run riot.
It was the only blot on an otherwise outstanding display from the 28-year-old, who underlined his status among the favourites for the Golden Boot as tournament top scorer with goals in each half to belatedly launch Spain's 2010 South Africa campaign.
Villa had already hit the crossbar from long range by the time he broke the deadlock with a memorable 17th minute strike, leaving three defenders trailing as he cut into the area to beat goalkeeper Noel Valladares with a thumping right-foot finish from 10 yards.
With Liverpool's Fernando Torres looking rusty as he continues his international rehabilitation following knee surgery, Spain had to wait until six minutes into the second half before deservedly doubling their lead.
Villa again applied the finishing touch, this time with the aid of a deflection off defender Osman Chavez to round-off a flowing four-man half the length of the pitch move as the hapless Hondurans were cut to shreds by some incisive passing and movement.
A third to more accurately reflect Spain's dominance should have arrived shortly after the hour as midfielder Jesus Navas was upended in the area by Emilio Izaguirre's lunge.
Inexplicably after such an outstanding display, Villa's low penalty thudded into the advertising boards behind Valladares' goal as the striker missed an opportunity to claim the tournament's second hat-trick.
In a group where the top two places are likely to be settled by goal difference, it is a miss that the Spaniards could be left to rue, especially as the runners-up are likely to face the favourites Brazil in the last 16.
After two straight defeats, Honduras' campaign is all but over and their main target in their final group game against Switzerland will be to end their 28-year wait for a goal in the finals.
There will be plenty more at stake as Spain tackle the group leaders Chile, with the winners going through, but the losers leaving themselves at the mercy of a victory for the Swiss.