The Dons always looked comfortable as they secured their fourth win in their last five games to move up to 16th in the table, seven points clear of the relegation zone.
Morecambe should have gone ahead after 26 minutes but Andrew Fleming contrived to shoot wide with the goal gaping after good work by Jack Redshaw.
It was Wimbledon who took the lead through Sainte-Luce in the 38th minute after a lovely flowing move.
Rashid Yussuff played Gary Alexander in behind the visitors' defence and the latter's left-wing cross was bundled home by 19-year-old Kevin Sainte-Luce from four yards out.
The hosts doubled their advantage six minutes later from the penalty spot when Chris McCready handled a powerful Alexander effort.
Jack Midson stepped up and his spot-kick into the bottom left-hand corner sent Morecambe goalkeeper Barry Roche the wrong way.
At the other end, John Sullivan had to be alert to tip a Jordan Burrow header over in the second half but the Dons held on for a vital win.