Conventional pear–kiwifruit wine has a bland flavor and sour taste, because of excessive l-malic acid content and, consequently, little consumer appeal. An Oenococcus oeni strain, GF-2, has good malolactic fermentation (MLF) performance and high glucosidase activity. Through a Box–Behnken design, the optimum MLF parameters for deacidification by GF-2 were determined: initial pH of 3.4, 5% v/v inoculation, and temperature of 20 °C, which reduced the malic acid content by 98.3%. The changes in the content of organic acids, polyphenols, and aromatic compounds after MLF were compared with chemical deacidification. MLF significantly decreased the total concentration of organic acids by 29.7% and promoted the accumulation of aromatic esters, higher alcohols, and terpenoids, but chemical deacidification markedly decreased aromatic compound content by 59.8%. MLF wine achieved the highest sensory scores for aroma, taste, and overall acceptability. Therefore, MLF with O. oeni GF-2 has great potential to markedly improve the quality of commercial pear–kiwifruit wine.