The purpose of the present randomized controlled clinical study was to compare the clinical outcomes of papilla preservation flap surgery with or without the application of a novel nanocrystalline hydroxyapatite (nano-HA) bone graft substitute. Fourteen patients with paired intrabony periodontal defects of ≥ 4 mm participated in this split-mouth design study. The defects in each subject were randomly selected to receive nano-HA paste in conjunction with papilla preservation flaps or papilla preservation flaps alone. Probing bone levels (PBL) from a customized acrylic stent and probing pocket depths (PPD) were measured at baseline and again 6 months following surgery. No differences in any of the investigated parameters were observed at baseline between the two groups. Healing was uneventful in all patients. Both treatments resulted in significant improvements between baseline and 6 months (p < 0.05). At 6 months after therapy, the sites treated with nano-HA paste showed a reduction in mean PPD from 8.3 ± 1.2 to 4.0 ± 1.1 mm and a gain in PBL of 4.3 ± 1.4 mm, whereas in the control group, the mean PPD changed from 7.9 ± 1.2 mm to 5.0 ± 1.2 mm and PBL gain was 2.6 ± 1.4 mm. Results demonstrated statistically greater PPD reduction and PBL gain (p < 0.05) in the test group as compared with the control group. In conclusion, after 6 months, the treatment of intrabony periodontal defects with a nano-HA paste leads to significantly improved clinical outcomes when compared with papilla preservation flap surgery alone.