David Villa almost had a perfect night as a goal in each half from the new Barcelona recruit helped Spain get their World Cup campaign back on track.
A wonderful individual effort in the first half was followed by a goal forged by brilliant movement off the ball in the second.
The only thing missing was the hat-trick to crown the performance as he sidefooted wide a second-half penalty and struck the crossbar early on.
The win was vital after the opening Group H defeat to Switzerland and Vicente Del Bosque's side finally looked to have settled into the tournament.
Honduras had an early escape when Emilio Izaguirre handled the ball in the box as Fernando Torres tried to flick it over his head, but Japanese referee Yuichi Nishimura waved play on.
Spain were even more unfortunate in the seventh minute when a 30-yard Villa shot smacked against the crossbar with goalkeeper Noel Valladares well beaten as the European champions came flying out of the blocks.
Real Madrid defender Sergio Ramos wasted a glorious chance when he headed over a Xavi free kick from the left from three yards out and Villa cut in from the left and fired wide after Xabi Alonso had cleverly switched the play.
Spain still looked a little nervy in defence after the Switzerland setback and a deflected Walter Martinez cross drew an unorthodox clearance with the knees by Iker Casillas.
Spain then gained the lead they deserved, though, with a stunning strike from Villa after 16 minutes.
Again the new Barcelona man had drifted out to the left, but this time he somehow manoeuvred the ball between Sergio Mendoza and Amado Guevara with supreme close control, cut inside Osman Chavez and at full stretch smashed an angled shot across Valladares into the top corner.
Torres showed he was still some way from rediscovering his killer instinct as he headed a Ramos cross into the turf and over and then fired wildly over after full-back Mendoza, run ragged by Villa, gifted possession to him.
Villa then caught the eye for the wrong reasons after lashing out at Izaguirre as the pair waited for a free-kick to come in, and he was fortunate to escape a booking or even a red card as Spain took a single-goal lead into the interval.
The second goal arrived within six minutes of the restart as Spain launched a counter-attack.
This time it was Villa's movement off the ball that proved key as he drifted back to the edge of the box to receive Navas' cutback from the right and his shot looped in off Chavez.
Ramos almost added the third seconds later with a right-foot toe-poke from the edge of the area and more goals looked on the cards.
Villa wasted a chance to complete a hat-trick from the penalty spot when he sidefooted wide after Navas made the most of some contact in the box from Izaguirre.
Cesc Fabregas was then given his first taste of the 2010 World Cup, coming on for Xavi to a wall of vuvuzela noise.
The Arsenal midfielder almost scored within seconds as Ramos played him in over the top, he rounded Valladares but Maynor Figueroa got back to clear his shot from an awkward angle.
Substitute Ramon Nunez was the first to try his luck for Honduras in the second half with a right-foot free-kick over the top midway through the half, and Torres was withdrawn with 20 minutes to go for Juan Manuel Mata of Valencia.
Mata was quickly into the action with a left-foot shot over from 20 yards as the Hondurans allowed him too much space and tried to turn provider for his old club colleague Villa with eight minutes left, swinging in a cross from the left which Figueroa had to divert for a corner.
Villa was again denied his treble as Mendoza blocked a late effort from yet another Navas cross.