Arsenal trailed 1-0 to Hakan Calhanoglu's fine goal when Welbeck went down in the area under minimal contact from the visitors' Ricardo Rodriguez and was controversially awarded the penalty from which he scored.
Former England captain Alan Shearer accused Welbeck of having "conned" referee Jonas Eriksson with a "blatant dive" while Brian McClair, his former Manchester United youth team coach, said that he felt "disappointed in Danny".
The Hitchin-born playmaker is frustrated at how negotiations have played out and believes he has proved his fitness this season with a number of accomplished performances at the heart of midfield, playing an integral part in Arsenal's run to the quarter-finals of the Europa League. "I will watch it again promise I will give you an honest answer", Wenger told BT Sport. "I will give Danny my opinion as well, no problem".
"The referee was the man of the match and I will never forget that".
However, things then took a turn for the better when Danny Welbeck won a dubious penalty, and duly converted it.
"I am happy to be back in the team". I can understand that, because I don't really know what it was. We have to keep going.
8 Atletico Madrid's Fernando Torres celebrates scoring a goal with teammates.
It was enough to persuade Eriksson to point to the spot and Welbeck, back on his feet, calmly stroked home the penalty for his first goal since January.
The Gunners went into the game with a healthy 2-0 advantage following an impressive win at the San Siro a week ago.
The tie was wrapped up as Xhaka unleashed a tame long-range effort which Gianluigi Donnarumma inexplicably could not keep out, instead pushing the ball into the corner of the net. But Arsenal put the result beyond doubt in the 71st minute thanks to a mistake from Donnarumma.
Victory ensured Arsenal reached a European quarter-final for the first time since 2010, while they werejoined in the quarter-finals by Atletico, CSKA Moscow, Lazio, RB Leipzig, Marseille, RB Salzburg and Sporting Lisbon.
"We will see", Wilshere replied when asked if he will be staying beyond the current campaign.