Background Plant mediated induced systemic resistance against the plant-parasitic nematode, M. incognita infecting tomato cv Pusa Ruby was evaluated on application of four nematicidal rhizobacterial isolates (Bacillus subtilis, B. pumilus, B. megaterium and B. cereus) as elicitors and compared with the application of a chemical nematicide, Velum Prime. Methods The bioefficacy trial was conducted in pots preinoculated with the above isolates followed by M. incognita inoculation tomato to observe the reduction in nematode infection at 60 days and effect on photosynthetic and transpiration rates. The mechanism of induced resistance was assessed using qRT-PCR for quantification of three key defense genes(PR-1b, JERF3 and CAT) at 0,2,4,8 and 16 days after inoculation (DAI). The defense enzymes viz., super oxide dismutase(SOD), polyphenol oxidase(PPO), peroxidase (PO), and phenylalanine ammonia lyase (PAL) were quantified. Results Significant reduction in per cent root galling viz. 84.21 in B. pumilus, 83.70 in B. megaterium, 91.95 in B. subtilis, 81.8 in B. cereus, was observed compared to control. The reproduction factor was the lowest (15.83) in B. subtilis, followed by B. pumilus (21.00), compared to 48.16 in control, with enhanced photosynthetic and transpiration rate. The defense genes, PR-1b, JERF3 and CAT were expressed at 2.5 to 7.5 folds in rhizobacterial treated plants, but not in Velum Prime treatment. The increase in enzyme levels (μmol/min/mg) for SOD was from 1.5 to 17.5, PPO from 2.1 to 7.8, PO from 1.8 to 10.2, and PAL from 1.8 to 8.7 during 0 to 16 DAI.