Against the odds, Arsenal suffered a 1-0 defeat and have plenty of work to do in the second leg, despite controlling the proceedings in Porto.
The first half was a slow and dull affair, with the only real moment of suspense coming from a sensationally missed double chance from Wanderson Galeno.
The Brazilian saw a powerful close-range strike hit the far post and rebound to him, while his follow-up effort was hit wide of the near post.
The second half saw much of the same, and the game never sprung into life, with Arsenal seemingly content to rely on set pieces as they tried to find a route to goal.
It looked like it was going to be a typical 'bore draw' until deep into stoppage time when a long-range curling effort from Galeno caught our David Raya and found the back of the net, sending the Estadio Dragao into pandemonium, as the Dragons secured a famous win late on.
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Story of the game
Porto manager Sérgio Conceição made just one (enforced) change to the side who beat Estrela Amadora 2-0 on Saturday, as Wendell replaced the injured Zaidu Sanusi in defence.
Mikel Arteta opted to use the same side who beat Burnley 5-0 at the weekend, but there was a notable presence of academy players on Arsenal's bench, including Ethan Nwaneri, James Sweet and Ayden Heaven.
Arsenal made the most of a slow and uneventful start to the game, and the Gunners looked to take early control of the game.
The hosts had the chance of the game in the 21st minute as Galeno blasted an effort from close range which was rebounded by the far post, only for the Brazilian to fire his follow-up effort wide of the near post, to somehow see the score remain level.
Arsenal continued to dominate the half and were trying to utilise set pieces, particularly corners, but had no such luck as the half finished level.
Second half
The second half so no real change in the proceedings as Arsenal continued to dictate play and enjoy the majority of possession, but proved ineffective offensively.
While they continually looked to capitalise from corners, Porto looked more than comfortable in defending them which left the Gunners frustrated and unable to find any promising routes to goal.
Perhaps due to only making one substitution in the game, Arsenal looked jaded as the game progressed which invited more pressure from the hosts, which is something that Arsenal did not want to contend with.
As the game looked to be petering out for a goalless draw, a wonderful long-range effort from Galeno caught Raya off-guard and nestled itself in the back of the net, securing a late victory for Porto to take to the Emirates next month.
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Player of the match - Wanderson Galeno
It was a truly special performance from Galeno, with the 26-year-old providing a regular threat to Arsenal's defence and, on another day, the Brazilian may have had a hat-trick.
While Raya did not cover himself in glory, Galeno's late winner was simply sublime and a strike that he will no doubt remember for years to come, especially if it proves decisive after the second leg.