Commercially pure copper was joined to a 1050 aluminum alloy by friction stir welding. A specific configuration where the tool pin was fully located in the aluminum plate was chosen. In such a situation, there is no mechanical mixing between the two materials, but frictional heating gives rise to a significant thermally activated interdiffusion at the copper/aluminum interface. This gives rise to the formation of defect-free joints where the bonding is achieved by a very thin intermetallic layer at the Cu/Al interface. Nanoscaled grains within this bonding layer were characterized using transmission electron microscopy (TEM). Two phases were identified, namely, Al2Cu and Al4Cu9 phases. The nucleation and growth of these two phases are discussed and compared to the standard reactive interdiffusion reactions between Cu and Al.