Howard put Wednesday ahead in the ninth minute with his first goal for the club since joining on loan from Hartlepool in March before Lita, another loanee, added a second after half an hour against his former club.
A crowd of 31,375 witnessed the game although many of them would have approached it with some trepidation.
However, they knew their destiny was in their own hands: win or equal Peterborough and Barnsley's results and they would be safe.
The influential Jermaine Johnson returned from a hamstring injury, one of three changes for the Owls with Lita and on-loan midfielder David Prutton both starting.
Boro have endured a miserable run of form that has seen them win just three times in 2013 and they will be glad to have limped across the line.
Top-scorer Scott McDonald and defender Christian Burgess returned to the starting line-up but there was no place for forward Marvin Emnes.
Johnson screwed an effort well wide after shrugging off the attention of two defenders and Seyi Olofinjana blazed over as Wednesday made their attacking intentions clear.
However, they were given a warning when Curtis Main escaped the defence and forced goalkeeper Chris Kirkland to smother at the Boro man's feet.
But Wednesday were in front in the ninth minute when Howard judged his run well and ran on to an incisive low ball before firing an unstoppable shot past Jason Steele.
Main was Boro's only threat and he screwed a shot across goal after twisting through the defence but the hosts were in the ascendancy, Johnson firing narrowly wide.
And they got their rewards after half an hour when Lewis Buxton's inswinging corner was glanced home by Lita in a packed six-yard box.
Wednesday's pace was troubling the visitors and they almost got a third moments later when only a desperate goal-line clearance prevented Howard from getting his second of the day.
Kirkland gathered a teasing cross in first-half injury-time but the break arrived with rapturous applause for Wednesday who had all but booked their Championship spot for next season.
Johnson did not return after the break but it could have been 3-0 shortly after the re-start when Lita pounced on a poor backpass but he hesitated slightly allowing Steele to come out and smother a shot which had neither direction nor pace.
Boro offered more after the break and Burgess headed narrowly over from Grant Leadbitter's corner.
Wednesday appeared to be content to play it safe and take few risks but it was allowing Boro to come on to them and Kirkland had to be alert to fingertip Leadbitter's low drive out for a corner.
Hillsborough held its breath when Rhys Williams appeared to be wrestled to the ground in the area but the referee waved away Boro protests.
The match was winding down before a clash of heads between Lita and Ben Gibson was cause for concern.
However, any fears were soon assuaged and the Wednesday fans soon got down to celebrating securing their Championship status - the final whistle prompting a pitch invasion.
- Sports & Recreation
- Chris Kirkland
- Jermaine Johnson