We applied a post-heat treatment to the tomato puree production process after vacuum microwave concentration, and investigated its effect on the flavor and nutritional components of tomato puree. The highest levels of glutamic acid and aspartic acid were confirmed in the tomato puree sample with post-heat treatment for 20 min. Among all samples analyzed, the scores for the sensory evaluations of “umami” and “total satisfaction” were the highest in the 20 min post-heated sample. Lycopene, a natural antioxidant in tomato puree, was isomerized from its naturally occurring stable all-trans form to the cis form by post-heat treatment. No negative effects on the L-ascorbic acid and DPPH radical scavenging activity were observed in the tomato puree at the post-heat treatment step. The results of this study suggest that tomato puree subjected to heat treatment after concentration by vacuum microwave treatment retains a good flavor and has a higher cis-lycopene content, which results in higher absorptivity.