Joining dissimilar sheet thicknesses of AA6082-T6 alloys by friction stir spot welding (FSSW) provides many advantages in automotive and aerospace applications. The formed keyhole at the end of the FSSW process is one of the typical features after the welding process, which owns the same size as the rotating pin that remains at the joint center. This keyhole destroys the joint continuity and can stimulate serious stress concentration when the FSSW joint bears an external force. To solve this issue, a novel refilling technique was developed for the FSSW keyholes using a friction stir deposition (FSD) technique. The FSSW joints of AA6082-T6 sheets were welded at various rotation speeds from 400 to 1000 rpm and a constant dwell time of 3 s, where a 2 mm sheet thickness was an upper sheet, and a 1 mm sheet thickness was a lower sheet. All the keyhole refilling processes were achieved using a specially designed AA2011-T6 consumable rod to be used for friction stir deposition of continuous layers at a constant deposition parameter of 400 rpm consumable rod rotation speed and a 1 mm/min feed rate. The heat input energy for both the FSSW and refilled FSSW lap joints was calculated. In addition, the FSSW and the FSD temperatures were measured. Macrostructure, microstructure, and mechanical properties in terms of hardness and tensile shear maximum load were evaluated for both the friction stir spot welded (FSSWed) and the refilled FSSW lap joints. The obtained results showed that the keyhole could be successfully refilled with defect-free continuous multilayers after the refill friction stir spot welding (RFSSW) process. All the RFSSW lap joints showed higher tensile shear loads than that given by the FSSW (before refill) lap joints. The RFSSW joint (welded at 600 rpm/3 s and refilled at 400 rpm/1 mm/min) showed a higher tensile shear load of 5400 N ± 100 compared with that recorded by the unrefilled joint (4300 N ± 80). The fracture location and fracture surface of the FSSW and RFSSW were examined and discussed.