Iker Muniain hit the post and substitute Rodrigo the crossbar amid a second-half Spanish onslaught, but Honduras battled heroically to keep Luis Milla's star-studded side at bay.
Bengtson got the game off to a sensational start when he climbed high to power Roger Espinoza's driven cross past Manchester United goalkeeper David de Gea.
One thing I can say is that tonight's match was certainly not typicalHonduras manager, Luis Suarez
Spain gradually worked their way into the game, with Chelsea's Juan Mata smashing a left-footed volley just wide and then going even closer on the stroke of half-time.
Espinoza might have deepened Spain's woe had his 51st-minute header not come back off the post, but Adrian Lopez hit the crossbar at the other end three minutes later with the Spaniards pressing Honduras.
Athletic Bilbao midfielder Muniain blasted just wide and then rattled the foot of the post after another enterprising run, but it took a flying save from goalkeeper Jose Mendoza to keep out Rodrigo's 72nd-minute header, and the striker headed against the crossbar eight minutes from time.
Spain’s coach Luis Milla said team were desperately disappointed after their loss on Sunday night.
'It is possible that our recent success did impact, but this is a team full of players that play at the highest level,' said Milla.
'As you can imagine, everyone is sad and everyone is disappointed.'
Honduras manager Luis Suarez was thrilled by the victory which gave his side a real chance of making the last eight heading into Wednesday's final group game against Japan.
He said: 'One thing I can say is that tonight's match was certainly not typical.
'We scored early and then perhaps due to our organisation and tactics, or perhaps due to their bad luck - things went our way, so we are happy, and we may well go on to qualify. But we have got to stay calm going forward into our next game. The next match is certainly going to be very, very hard.'