"My game doesn't give him any rhythm since I mix up my game so much," said El Aynaoui, who extended Ferrero's semifinal drought to six events.
No. 3 Marat Safin of Russia avoided another upset, managing to rally for a 2-6, 6-4, 6-4 victory over Max Mirnyi of Belarus.
El Aynaoui extended his ATP winning streak to eight matches. In his previous tournament, the 30-year-old won his second career title at the Gelsor Open in Bucharest.
"In the beginning, I didn't notice that anything was wrong with Jonas," Malisse said. "Then, at 2-1 in the first set, he hardly ran, and I knew that things were bad."
Malisse is gunning for his third finals berth of the year, having reached the championship match at Atlanta and Delray Beach.
Safin has won two of his three meetings with Mirnyi in 2001. After losing their contest at Rottendam in February, Safin exacted revenge in the second round of last week's Kremlin Cup.
"With his serve and volley, it's difficult to get any rhythm," Safin said. "In the first set, he served well and I had no chance. But I stayed in the match and I fought."
Safin will attempt to capture his second title in a month after not lifting a trophy during the first two-thirds of the year. He claimed the President's Cup at Tashkent, Uzbekistan.
Safin's semifinal opponent will be Ivan Ljubicic of Croatia, who pulled away to beat Gaston Gaudio of Argentina, 6-3, 6-7 (5-7), 6-1.