During the match in Porto, two Video Assistant Referee (VAR) decisions went against the Serie A side in the final minutes.
FC Porto were awarded a penalty kick late in extra time following a VAR review.
Alex Telles converted it to give them a 3-1 win on the night in the round of 16 second leg tie and push them through 4-3 on aggregate.
Shortly afterwards, AS Roma forward Patrik Schick went down under a challenge from Moussa Marega in the FC Porto area.
But the referee, who consulted the video assistant and did not review the incident himself, waved play on.
“Last year we asked for VAR in the UEFA Champions League because we got screwed in the semi-final and tonight, they’ve got VAR and we still get robbed,” Pallotta posted on the club’s official Twitter feed.
“Patrik Schick was clearly clipped in the box, VAR shows it, and nothing is given. I’m tired of this crap. I give up.”
UEFA, the European football governing body, could not immediately be reached for comment.
There was no immediate comment from AS Roma on the future of coach Eusebio Di Francesco, who was already under pressure after a 3-0 derby defeat to Lazio on Saturday.
Di Francesco did not speak to the media after the game, instead going straight to the team bus.