The hosts dominated the first half and took the lead through Dean Shiels’s cool finish.
But the Irish spurned several openings, the best of which fell to Chris Brunt, who struck the outside of the post from close-range.
Moments later Luxembourg denied Michael O’Neill’s side all three points with a heavily deflected shot by Da Mota.
Having lost in Moscow at the weekend, Northern Ireland were looking to get their World Cup qualifying campaign off the ground with victory against a side now ranked 23 places above them in the world rankings.
Luxembourg started well but it was only a matter of time before they would come under pressure, and Northern Ireland were dealt a blow when Shiels was wrongly flagged offside with just goalkeeper Jonathan Joubert to beat.
But Shiels was celebrating moments later as he lifted the ball over the keeper to put the hosts ahead after a good run and through ball by Manchester United centre-back Jonny Evans.
The goal lifted the home fans and Northern Ireland thought they had doubled their lead in the 21st minute, but Evans’s headed goal was harshly ruled out for a shove by Kyle Lafferty in the build-up.
The hosts had yet another goal chalked off, this time legitimately, as Lafferty was offside as he received the ball from Brunt before brilliantly sweeping it into the top corner.
But Northern Ireland grew in stature as the half progressed and could have sneaked further ahead when Chris Baird glanced Brunt’s corner a foot the wrong side of the post.
The second half was far scrappier, littered with yellow cards and petulance as Luxembourg tried to disrupt Northern Ireland’s rhythm.
They succeeded to an extent as the home side lacked discipline as they were flagged offside over a dozen times.
On one of the few occasions Northern Ireland beat the offside trap, Brunt could only strike the post when he should have put the game beyond doubt.
The sting in the tail that the home side feared became a reality moments later, as Da Mota seized on the loose ball and saw his shot take a huge deflection off Ryan McGivern and cruelly diverted beyond Roy Carroll.
It was harsh on a gutsy Northern Ireland side that deserved better. They now face a trip to Portugal, and will be without defender Gareth McAuley who collected a yellow card and a one-match suspension.
Elsewhere in Group F, Silvestre Varela again proved his worth by coming off the bench to break the deadlock with his first touch and set Portugal on their way to a 3-0 win over Azerbaijan.
After much frustration and wasted chances for the Portuguese, Varela slotted home in the 64th minute. The winger also made a big impact as a substitute in Euro 2012 when he scored to secure a last-gasp group stage win over Denmark in June.
Portugal were never sure of victory on Tuesday until striker Helder Postiga and defender Bruno Alves scored in quick succession in the last five minutes.
Braga's distinctive "Quarry" stadium welcomed 30,000 fans who were not disappointed by the home side's attacking display, but were made to wait anxiously for a goal.
Azerbaijan, forged in the steely ways of their coach, former Germany defender Berti Vogts, fought resiliently and kept the hosts at bay in the first half.
But Portugal, now with two wins from two in Group F, kept pressing on and were rewarded eventually when substitute Varela picked up a loose ball that was fumbled away from a Cristiano Ronaldo effort and drilled it in.
Impressive Russia made it two qualifying wins from two under Fabio Capello after Alexander Kerzhakov scored twice in a 4-0 demolition of Israel.
Russia, criticised at home for not scoring more in their 2-0 win over Northern Ireland in Moscow on Friday, produced an assured and clinical performance on a warm, humid night in Tel Aviv.
Kerzhakov scored his first from a free kick after seven minutes and fellow striker Kokorin doubled the lead 11 minutes later.
Kerzhakov broke free of Israel's disorganised defence to slot home his second on 64 and substitute Victor Fayzulin was left unmarked to complete the rout.
Defeat for Israel was one of the worst they have suffered at home in the past two decades and dealt a severe blow to their qualification hopes for Brazil 2014 after they managed a 1-1 draw against Azerbaijan in Baku on Friday.
It marked a continued bad run for Israel's new coach, Eli Guttman who has yet to win any game since taking over last December, having lost four matches and drawn two.