Laboratory studies were carried out to isolate, identify and control the fungi associated with fruit rot of tomato (Lycopersicon esculentum). Aspergillus viridae, Penicillium digitatum and Rhizopus sp were isolated from samples collected from Lokoja, Kabba, Okene, Anyigba and Ankpa, all in Kogi State, Nigeria. Plant extracts employed to control the vegetative mycelial growth were from neem (Azadirachta indica) and tobacco (Nicotiana tabacum) at 20%, 30%, 40%, 50% and 60% concentrations. In vitro application of extracts for the control showed that tobacco (Nicotiana tabacum) had fungitoxic effect that controlled the mycelia growth; there was complete inhibition (0.00 + 0.00) at 60% on Aspergillus viridae and Penicillium digitatum. Tobacco extract on Rhizopus showed progressive retardations on the vegetative growth. Vegetative growth of the fungi on neem extract decreased with increase in concentrations; with its effect (extract) being felt more on Penicillium digitatum at 60% concentration (0.41 + 0.55) when compare with the control. The inhibitory action of the two extracts on mycelial growth increased with increase in concentrations; giving toxicity profile of 60% > 50% in that order, and were significant at 0.05%.