Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Sacc.) W.C. Synder and H.N. Hans is the major limiting factor in the production of tomato. An effort was made to develop an eco-friendly approach to control Fusarium wilt in tomato using fluorescent Pseudomonas, Trichoderma harzianum and Glomus intraradices, an arbuscular mycorrhizal fungus (AMF). Besides direct interaction with plant pathogens, bioagents have been reported to induce systemic resistance in plants. In the present study, a large number of Trichoderma sp. and pseudomonad isolates were evaluated for their efficacy to control Fusarium wilt of tomato. T. harzianum was multiplied on six different substrates out of which Jhangora, an undertilized grain crop, proved to be the superior substrate. Application of T. harzianum and fluorescent Pseudomonas by seed bio-priming significantly increased seed germination (22–48%) and reduced the days required for germination (2.0–2.5 days). All bioagents used in this study significantly reduced the incidence of wilt in pot and field trials and combinations of bioagents were more effective than single isolate treatments. The combination of fluorescent Pseudomonas, T. harzianum and AMF provided significantly better control than uninoculated treatment, reducing disease incidence and severity by 74% and 67% in pots and field, respectively. The combination treatments also increased yield by 20%. Addition of cow dung compost (CDC) further reduced disease and improved yield in all treatments. Comparing to control (-CDC), the combination of all three bioagents with CDC significantly reduced disease by 81 and 74% in pots and field, respectively and enhanced the yield by 33%.