But he slid home Theo Walcott’s cross deep into added time to devastate the Magpies, putting Arsenal firmly on course to overthrow their north London rivals.
The Gunners fell behind for the fourth Premier League game in a row when Hatem Ben Arfa got the better of Kieran Gibbs in the 14th minute before squeezing his shot past Wojciech Szczesny at the near post.
They were quickly level though, when prolific captain Robin Van Persie fired home from close range one minute later after good work from Walcott on the right wing.
And just when Newcastle looked to have battled to a share of the spoils, Vermaelen’s goal left them empty handed.
Alan Pardew’s side remain sixth with a five point cushion over Liverpoool in seventh, but trail Chelsea by the same number of points.