After AFC Wimbledon's Jack Midson had cancelled out Stephen Gleeson's 30-yard scorcher, visiting fans spilled onto the pitch near Martin's goal.
Martin, who played two matches for Wimbledon before the club's high-profile move to Milton Keynes, then broke the League Two side's hearts by denying Steven Gregory one-on-one late on before Jon Otsemobor's flicked late winner.
Tensions ran high throughout the first ever meeting between the two sides and although MK Dons fans also invaded the pitch, Martin was unfazed.
Asked what it was like being in front of the Wimbledon fans, Martin said: "It wasn't too bad, I thought I was going to get worse to be honest.
"It was a bit hairy when they came onto the pitch when they scored but they were reasonably well behaved.
"You can understand the emotions that surround this game that will overflow sometimes - when they scored obviously it was a great moment for them.
"But they didn't really show any aggression towards me, so I was happy enough just to back off.
"It would have obviously been a fairytale for them to be going 2-1 up in the last minute but I'm employed by MK Dons and the chairman here.
"So it's a great thing to make a difference for any team that you play for, let alone in a big game like this that is unique."