Jonker was formerly in charge of the Gunners academy before leaving for the top job at Wolfsburg, where he had the Swede as his No2.
He told Sky Sports: "I would support the guts in making the choice (to hire) Freddie Ljungberg. Arsene had been there many, many years and he did it his way. Then came another coach (with a different way) who had a very difficult time.
"I would prefer for them to give the chance to someone who knows Arsenal, knows the academy, knows all those talented players. He also knows the laws of total football.
The Dutchman also revealed: "The reason I brought him to Wolfsburg (was that) I wanted to have someone with an eye for individual development of players.
"(He has) this strategical mind. He wants to think about tactics, how we beat the opponent.
"I decided that he is a very talented coach. He had to find his way from the (Arsenal) under-15s, to Wolfsburg, to the under-23s. I can imagine now that he is ready now to the (Arsenal) job, he is a very talented coach. I think that's why he got this chance."