Shakhtar looked destined for victory after Luiz Adriano tapped in with five minutes to go to add to the lead given to them earlier in the second half by Alex Teixeira.
However, Porto, who had a Yacine Brahimi first-half penalty saved by Andriy Pyatov, staged a stunning late fightback.
And Porto claimed the unlikeliest of points when Martinez, who had been introduced in the 65th minute, stole in at the near post to finish Cristian Tello's low cross in the 93rd minute.
The draw extends Porto's unbeaten start to the season and gives them a point to add to the three they earned in the first round of Group H matches, courtesy of their 6-0 home win over BATE.
While Porto took full advantage of the numerous chances that came their way against BATE, Julen Lopetegui's men were wasteful in the extreme at Shakhtar on Tuesday until the dying moments.
Perhaps assisted by the fact that this game was played 760 miles away from Shakhtar's Donbass Stadium as a result of the unrest in Ukraine, Porto played with far greater authority than expected for an away side.
Midway through the half, Porto were given an even better chance to open the scoring when they were awarded a penalty for Oleksandr Kucher's trip on Brahimi.
Porto's chance of claiming anything from the game looked to have gone with five minutes to go when Shakhtar hit them on the break and Adriano tapped home Bernard's pass at the back post.
However, Porto refused to give in and their persistence was rewarded when Rakitskiy handled in the box and Martinez slotted home from the spot before the same player found himself in the perfect place to tap in and rescue a point with the 2-2 draw.
