Ferrer, ranked fourth in the world, tumbled to the Belgian grass court specialist 7-6 (7-3), 6-3 in the opening round at Autotron Rosmalen.
The Spaniard was seeking to repeat in the Netherlands after downing German Philipp Petzschner in last year's finale.
Malisse, meanwhile, notched just his 16th win 57 all-time matches against Top 10 players.
Elsewhere Tuesday, second-seeded Stanislas Wawrinka of Switzerland moved on to the second round with a 7-6 (7-5), 6-4 defeat of Belgian lucky-loser Steve Darcis 7-6 (7-5), 6-4, while No. 5 seed Jeremy Chardy of France bested countryman Lucas Pouille 7-5, 6-4.
The news wasn't as good for No. 4 Benoit Paire, who retired in the first set against French countryman Michael Llodra.