Understanding the origin of magnetic ordering in an undoped semiconductor with native defects is an open question, which is being explored actively in research. In this investigation, the interplay between magnetic ordering and excess induced native defects in undoped anatase TiO2 nanoparticles is explained using an experimental and theoretical approach. It is demonstrated that structurally disordered TiO2 nanoparticles with a high concentration of native defects such as titanium interstitials and oxygen vacancies are synthesized using controlled atmospheric rapid cooling (i.e. quenching) process. The structural disorders in the lattice have been examined using various spectroscopic and microscopic analyses revealed the existence of Ti deficiency in both pristine and quenched TiO2 nanoparticles. A possible origin of magnetic ordering in titanium deficient anatase TiO2 system is elucidated based on first-principle calculations. It was found that the overall magnetic moment of Ti deficient TiO2 system is determined by the distance between Ti interstitials and its neighboring vacancies (i.e. either V Ti or V Os). However, quenched TiO2 nanoparticles possess excess Ti interstitials, Ti and O vacancies and therefore the net magnetic moment of the system is reduced due to anti-ferromagnetically coupled neighboring Tilattice ions.