Needing a win in Lucerne to top the group, Theo Walcott had lobbed England ahead before David Nugent doubled the lead.
However, the impressive Johan Vonlanthen, who was injured for the World Cup, pulled a goal back from the penalty spot before Tranquillo Barnetta curled in an equaliser, with the Swiss in command until Milner struck with two minutes remaining.
The Newcastle player is apparently still smarting over his last second transfer to Aston Villa being blocked by chairman Freddy Shepherd. And Birmingham newspapers reported yesterday that it was a childish ploy by Shepherd to hit back at a snub by Villa boss Martin O'Neill.