Sweden manager Jon Dahl Tomasson had called for a reaction from his side after Saturday's defeat in Luxembourg, and the hosts responded.
After half-chances for Justin Devenny and Ruairi McConville, the hosts took the lead in the seventh minute.
Isak danced his way across the edge of the area and shaped to shoot on a number of occasions, which dragged the Northern Ireland defence towards the ball and that left Holm all the time and space he needed after the Newcastle forward found him in the area.
With the wind in their sails, Nygren and Isak fired over from inside the area, and Price went close at the other end when he drifted inside and let fly from 25 yards but Viktor Johansson made a simple save.
In a good spell for Northern Ireland, Brodie Spencer was inches away from levelling the game as he curled narrowly over from inside the area, but despite their pressure the Swedes soon doubled their lead.
Gabriel Gudmundsson got in behind the Northern Ireland defence and played in a low cross, which Pierce Charles pushed straight into the path of Nygren, who had the simple task of tapping in for his first international goal.
Paddy McNair had to be alert to cut out another cross, this time from Holm as Isak looked ready to pounce, but the visitors rallied and were unlucky not to pull a goal back before the break.
Shea Charles fired straight at Johansson after the Stoke City goalkeeper played a poor pass straight to the midfielder, but the keeper redeemed himself moments later when he produced an acrobatic save to push George Saville's goal-bound effort over the bar.
Captain Charles went close again in the area but his strike was diverted wide by Isak and McConville headed off target after finding himself in space from the resulting corner.