The Cameroon forward was one of nine changes made to Julen Lopetegui's starting XI, given that they had already secured first place in Group H and have a top-of-the-table clash with Benfica on Sunday in the Primeira Liga.
Aboubakar responded by thundering the ball home from the edge of the box three minutes from time, ensuring Porto went through to the last 16 as one of only three unbeaten teams, alongside Real Madrid and Chelsea.
"I'm satisfied," the 22-year-old told Sport TV. "I scored a goal and we're on the right path.
"I was in a good position and I saw I had space to shoot. It was a great feeling to see it go in."
Jackson Martinez has been prolific at the Porto spearhead this season, scoring 16 goals in all competitions, but Aboubakar hopes his performance against Shakhtar will afford him more opportunities.
"The most important thing for me is to get playing time," he said.
"Will I start the next game? The coach will decide."
Playmaker Ricardo Quaresma saluted Porto's ability to keep going until the end.
"We're a side who always has faith until the end, and that's what happened today," he said. "We equalised just before the 90 minutes were up and could have scored a second but didn't manage to.
"We deserve congratulations. We gave it everything we had.
"Our goal was to finish first in our group, and we did. Now we have to continue working and think about our next game."
