A novel enzymatic process was established for galactooligosaccharides (GOS) synthesis by using plant-derived galactose as substrate, without producing any byproducts. The galactose was prepared from the acid hydrolysate of gum arabic. The yeast Kluyveromyces lactis producing β-galactosidase capable of catalyzing GOS synthesis from galactose was screened out. The synthesis conditions using the yeast cells as enzyme source were optimized by both single-factor experiment and response surface methodology, with the highest GOS yield reached 45%. The composition of reaction mixture contained only GOS and unreacted galactose, which could be easily separated by the cation exchange resin column. The structures of major GOS products were identified as Gal-β-D-(1→6)-Gal, Gal-β-D-(1→3)-Gal, and Gal-β-D-(1→6)-Gal-β-D-(1→6)-Gal by MS and NMR spectra. Moreover, the β-galactosidase-containing cells can be recycled for at least 30 batches of GOS synthesis at 35°C, with the enzyme activity remaining above 60%.