Prosopis juliflora is a small weed tree, native to Central and South America, and the Caribbean, which has become a major invasive weed in Asia, including India, Latin America, Africa and Australia. It has major detrimental impact on scarce, underground water resources, takes over the local flora ecosystems and affects the soil environment. Manual removal of saplings is time-consuming and expensive. Presently, the removal of the weed is performed manually which is time-consuming, or using very expensive commercial heavy equipment. In this paper, an affordable and innovative unmanned aerial vehicle (UAV) unmanned ground vehicle (UGV) system is designed and developed for autonomous identification and removal of the weed seedlings and saplings. Results of implementation of a proof-of-concept prototype system using mainly commercial off-the-shelf components, open source hardware and free open source software, are presented to illustrate the effectiveness of the proposed approach.