Michael O'Neill's side dominated the first half but couldn't find a breakthrough and were duly punished by the home side.
Sports Mole takes a look at the action in Baku to see if the home side deserved their first competitive victory since September 2011.
On target 4
On target 8
Was the result fair?
The game was decided by the side that took their chances when they were presented with them, and Vogts's team did just that as they dominated the second half and showed it with two decisive strikes. Meanwhile, O'Neill's side were in command of the first half but came away with nothing to show for it. It's a cliche but this game is decided by how you perform in front of the net and Azerbaijan certainly deserved to win by taking their chances when presented with them.
The home side were always a threat going forward. They had half-chances in the first half but were unable to get a grip on the game until after the break. Defensively they were suspect and were indebted to a great performance from keeper Kamran Agayev as he denied the visitors on several occasions until his teammates managed to get on a grip on the game. When they scored their opener they took command as O'Neill's side struggled to impose themselves after that. Vogts's team were clinical where the Irish weren't and that is what decided the game.
Northern Ireland's performance:
O'Neill's side just lacked the clinical edge they needed in front of goal. They created a plethora of chances in the first half but couldn't take any of them while they dominated possession as well for the majority of the game. Their poor finishing in the opening period exposed them after the break when the home side picked them apart with a fine move, then frustration kicked in and it all looked a bit desperate from 60 minutes onwards. Martin Paterson was unlucky to see his effort smack off the post but apart from that they offered very little.
Sports Mole's man of the match:
Mahir Shurukov: This could have gone to the right-back or his side's keeper Agayev, but the defender's goal at the end of the game with a fine strike into the top corner just secured the berth. The 30-year-old defended stoutly when he needed to and was an attacking threat all evening as he lifted some excellent crosses into the area which almost gave Dadashov a strike before he found the net minutes later. A complete performance from the veteran.
Jamie Ward should have given O'Neill's side the lead in the first half when he latched on to Lee Hodson's cross but somehow he smashed an effort over from four yards away from goal. He was not the only one as Paterson missed a similar effort minutes later but the his was slightly worse than his teammates and not one he will like to remember.
Andre de Marco's performance was fine for the most part. There were a couple of decisions here and there when he was duped by some play-acting from the home side. The Italian got the sending-off of Jonny Evans spot on as he noticed his kick out at Aliyev. A strong performance all round.
Azerbaijan: Vogts's side will face Russia in Baku to end their qualifying campaign.
Northern Ireland: O'Neill's side will travel to take on Israel in their final game.