Pompey suffered a rare home defeat as MK Dons left the south coast with all three points.
Bradley Johnson and Jack Tucker netted in each half to settle the contest in favour of the struggling visitors.
Danny Cowley's side were unable to make the most of several opportunities before the break and had a Josh Koroma goal controversially ruled out after it.
Fans can watch the key moments (top video) or register with iFollow for extended highlights (middle video) and a full match replay (bottom video).