Biocatalysis has developed in the last decades as a major tool for green polymer synthesis. The particular ability of lipases to catalyze the synthesis of novel polymeric materials has been demonstrated for a large range of substrates. In this work, novel functional oligoesters were synthesized from ε-caprolactone and D,L/L-malic acid by a green and sustainable route, using two commercially available immobilized lipases as catalysts. The reactions were carried out at different molar ratios of the comonomers in organic solvents, but the best results were obtained in solvent-free systems. Linear and cyclic oligomeric products with average molecular weights of about 1500 Da were synthesized, and the formed oligoesters were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The oligoester synthesis was not enantioselective in the studied reaction conditions. The operational stability of both biocatalysts (Novozyme 435 and GF-CalB-IM) was excellent after reutilization in 13 batch reaction cycles. The thermal properties of the reaction products were investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) analysis. The presence of polar pendant groups in the structure of these oligomers could widen the possible applications compared to the oligomers of ε-caprolactone or allow the conversion to other functional materials.