As expected, the reigning world champions dominated possession, with Northern Ireland seemingly content to sit back and attack on the break.
Mario Gotze had an opportunity from eight yards out, but his header was punched clear by goalkeeper Michael McGovern, who did not have too much to do during the first half, despite Germany's dominance.
The breakthrough was made in the 13th minute when Draxler, who was given plenty of space on the edge of the box, curled the ball into the bottom corner past McGovern, who got fingertips on it.
The second goal came from a corner kick, which resulted in Mats Hummels nodding towards goal and Khedira getting a touch to nudge the ball into the back of the net.
Northern Ireland created little going forward, but they looked dangerous when they did. One opportunity fell to Jamie Ward, whose shot from inside the box deflected wide.
Magennis showed attacking intent throughout the match, and he came close to getting on the scoresheet when he worked the ball around Hummels before firing at Neuer from a tight angle.
A few minutes after Gotze was disallowed a goal, Germany had a nervy moment when Corry Evans was awarded a free kick right on the edge of the box after getting brought down by Jerome Boateng, but the resulting set piece was sent over the bar by Oliver Norwood.
After the break, Northern Ireland jumped out of the blocks thanks to a storming run from Ward, but it did not take long for Germany to find their stride again.
Lee Hodson made a crucial clearance to prevent a third goal in the 55th minute after Boateng's chipped pass over the top found Gotze, who headed into the six-yard box for Thomas Muller to tap in, but the Irish defender got there first.
A few minutes later, Germany had penalty claims denied when Kimmich went to ground following a challenge from Shane Ferguson, but it appeared as though the referee made the right call.
The visitors did well to stifle their opponents by preventing them from finding a way through the middle, but full-backs Kimmich and Jonas Hector had plenty of joy down the flanks.
Khedira squandered an opportunity to score his second of the night when he sent a free header from six yards out over the crossbar, but he was not left to rue the miss as Germany peppered Northern Ireland's goal until the full-time whistle.
Despite the defeat, Northern Ireland's hopes of qualifying remain intact as they sit third in the group, three points behind second-placed Azerbaijan, while Germany top the standings with a two-point lead.