Dutchman Jonker returns to Wolfsburg three years after leaving his role as assistant manager to join Arsenal.
“I’ve remained in contact with Wolfsburg, but the inquiry did come as a bit of a surprise,” said Jonker, 54, at a news conference on Monday.
Former Arsenal forward Freddie Ljungberg will be Jonker’s assistant.
“This is a huge challenge,” he added. “All that counts is getting the 40 points as quickly as possible.”
Ismael was sacked on Sunday – two days after a 2-1 home defeat by Werder Bremen, their fourth loss in five league games, left them on 22 points with 12 games remaining.
Wolfsburg are 14th in the 18-team table.
Jonker’s first match in charge is at 11th-placed Mainz on Saturday