The 29-year-old has traded Old Trafford for Emirates Stadium after being used in a swap deal which took Alexis Sanchez in the opposite direction.
He was deemed surplus to requirements by United after slipping down the pecking order, with Mourinho having once again taken the decision to favour other options.
Petrosyan believes his star turn was unfairly treated by the Red Devils, but feels a move will prove beneficial to all concerned as Mkhitaryan is now at a club where his obvious ability will be embraced.
The Armenian national team boss told reporters: “I think Henrikh had a problem with the United coach and at Arsenal, it will be another thing and not the same situation. There will not be so much pressure on him defensively.
“Yes, he [Arsene Wenger] likes them to play better football. I think Wenger is better for Henrikh.
“We are very happy with this transfer from Manchester United. His style of play will be better suited at Arsenal.
“I only spoke with Miki and I cannot tell you about my talks with Miki because it was between us, but I told you about my impression that I was not happy with Mourinho.
“I think Henrikh can do very well in the Premier League. He can continue in a good mood, in a good way. He is always one of the best players in the Premier League but under this manager – Wenger – he will become even stronger.”
Petrosyan added on a testing period for Mkhitaryan at Old Trafford which saw him win three trophies but endure regular spells out of the team: “I think the [Manchester United] fans liked him. I think that means he did something for the club.
“I am not happy with Mourinho’s decision not to play him, but it is his club, his team — he knows what he wants. It is good he has left.”
Mkhitaryan is having to be patient as he waits to be handed his Arsenal debut.
An early FA Cup exit also means that the Gunners have no fixture this weekend, with their next outing coming against Swansea in the Premier League on Tuesday.