Having arrived at Baku's Bakcell Arena hoping to show last month's loss to Luxembourg was a blip, Michael O'Neill's side instead added another depressing result to their Group F hall of shame.
Yet at the half-time break, it seemed as though they were well set to claim a positive result.
Paterson and strike partner Jamie Ward both got on the end of good opportunities but could not provide the killer touch.
And although they went in at the interval confident their luck would change, the hosts pounced with a 58th minute goal from Rufat Dadashov and it only got worse from there.
Paterson lashed the woodwork with a powerful strike in the 88th minute and as the game entered added time Jonny Evans was sent off for a professional foul, as well as conceding a free-kick which Mahir Shukurov bent into the top corner.
Huddersfield forward Paterson revealed the players struggled to get their heads around their fate.
"If you watched that game you're probably scratching your head wondering how have we lost 2-0. We are," he said.
"People might see the result and say 'Northern Ireland lost 2-0, what a poor result that is' but they don't see how we've played.
"Saying that, we've only got ourselves to blame. We dominated the game for 45 minutes but didn't take our chances and their goalkeeper played very well.
"Then we just switched off for a couple of minutes, conceded, and the game changes.
"In the second half I hit the bar - it's a game of inches - and their second goal was just frustration.
"We can't look to blame anyone else other than who was out there."
After a night that proved a body blow to the team's hopes of a bright finish to their campaign, Paterson still felt able to tentatively look on the bright side.
With two points taken from a possible 12 against Luxembourg and Azerbaijan in the campaign, that might seem a stretch, but the 26-year-old gave it his best.
"There are positives to take, as mad as that sounds," he said.
"I don't think we're miles away but it's a fine line. We had four or five good chances, they got one break and scored: that's international football.
"But we are still a young group. We've got to learn quickly and turn results around. If we do we have a chance of really pushing in the next campaign, but we have to work harder as a unit."
Manager Michael O'Neill, who cut a frustrated figure in his post-match media duties - witheringly telling one local journalist they had posed "a stupid question" - now faces the unenviable challenge of lifting a depleted squad for Tuesday's final match in Israel.
Joining Evans in being suspended for that match are defensive talisman Gareth McAuley and midfielder Oliver Norwood, who each picked up their second bookings of the campaign.
Northern Ireland are unlikely to add to their squad in Tel Aviv, leaving O'Neill to sift through his current group for answers.
"We have three players out but we also have men to come in - particularly the likes of Sammy Clingan and Chris Baird," he said.
"We'll have to look at the centre-back situation because of the players we've lost to suspension and that is self inflicted.
"But I thought the referee was not strong enough. I'm disappointed with him, he should have been stronger on the night."
- Sports & Recreation