In the shadow of the Rock of Gibraltar, O'Neill's youthful Northern Ireland started well in the hot conditions and pressed from the off.
Their early pressure was rewarded when Atcheson, still up from a corner, reacted well to Price's teasing cross to flick home the opening goal.
The 19-year-old, who played under O'Neill at Blackburn Rovers, made his international debut as a substitute against Wales in March and marked his first start with a goal.
Guinea, ranked 80th in the world and without star Borussia Dortmund striker Serhou Guirassy, responded well to the early goal and Pierce Charles was the busier of the two goalkeepers.
Mohamed Toure's shot from the edge of the area forced Charles to tip over the bar, and Ruairi McConville had to produce a strong block to deny Traore.
Ibrahima Sory Bangoura was the next to test Charles, who clawed a goal-bound effort away, and Toure blazed over from the follow-up chance.
Like in the first half, Northern Ireland started well after the restart despite three changes from O'Neill, as goalkeeper Luke Southwood, Brodie Spencer and Reid were all introduced.
Donley, now playing on the right after the introduction of Reid, forced Soumaila Sylla into a low save from the edge of the area.
There was a big scare moments later when Ibrahima Breze Fofana's close-range header was saved by Southwood and Traore poked the rebound towards goal, but McConville got in the way to block the ball on the line.
The game then took a turn when Atcheson brought down Traore in the 72nd minute, earning the red card which rules him out of the France game on Monday.
Down to 10 men, Reid missed a glorious chance to put Northern Ireland two up when O'Neill's powerful effort was saved by Sylla and the Stevenage striker could not beat the goalkeeper from six yards.
Northern Ireland survived a scare in injury time when Southwood tipped Kourouma's powerful effort on to the crossbar as Guinea ended the game with 14 attempts to Northern Ireland's nine, but it was O'Neill's young side who held on to win.
