The Shrimps striker began a fine day by giving his side the lead after seven minutes of the League Two encounter.
Steven Gregory lost possession in the middle of the park and Ellison took full advantage as he sped past Callum McNaughton and produced a cool finish to beat Neil Sullivan.
Ellison doubled his side's advantage on 33 minutes with another smart finish. Stewart Drummond played the ball in behind a flat defence and Ellison again beat Sullivan.
The visitors gave themselves hopes of a second-half comeback when they reduced the deficit with a penalty. Jack Midson was brought down by Jordan Mustoe and the striker dusted himself down to send Barry Roche the wrong way from the spot.
The goal gave the Dons a life and a minute later Jake Reeves tested Roche with a well-struck effort from 25 yards. But their hopes of claiming something from the game were dashed when Ellison grabbed the matchball with a superb left-footed finish after 78 minutes.
To make things worse for Wimbledon, Paul McCallum was shown a straight red card in the 82nd minute for a late foul on Nick Fenton.