Chilling injury (CI) in peach fruit (Prunus persica cv. Yuhualu) is generally caused by long-time low temperature (5 °C or 0 °C) storage. However, peach fruit stored at near-freezing temperature (NFT in this research is −1 °C), defined as within 0.5 °C above the biological freezing point of biological tissue, does not exhibit CI symptoms. The effect of NFT on the CI, proline metabolism, and antioxidant capability of peach fruit during storage was studied and compared with 5 °C and 0 °C storage as controls. The results exhibit that NFT completely inhibited the occurrence of CI in peach fruit. NFT significantly (p < 0.05) enhanced the activities of superoxide dismutase, catalase, ascorbate peroxidase, and 1,1-diphenyl-2-picrylhydrazyl scavenging capacity. Moreover, the increase of malondialdehyde, ion leakage, and H2O2 accumulation were inhibited remarkably by NFT, and decreases in the contents of phenolics and ascorbic acid were slowed significantly in peach fruit stored at NFT (p < 0.05). Additionally, NFT storage enhanced proline accumulation by modulating the activity of proline metabolizing enzymes. In conclusion, the above results suggest that NFT storage can improve the chilling tolerance of peach fruit by regulating the antioxidant defense and proline metabolism, which might represent a potential novel method to store fruits and vegetables for longer storage times.