University education is in a process of change ready to take on the challenges of educational innovation by incorporating new technological tools to replace traditional ones; because, educational innovation must be reflected in educational practices that improve teaching learning. It is important to raise those technological tools in a requirement in virtual teaching. The professors Peruvian public universities of the Amazon present serious deficiencies to differentiate the digital and virtual tools of the traditional slate, multimedia projector and other resources that have supported teaching for many decades in the classroom. The objective of the research was: To determine the relationship between the use of technological tools in virtual education and educational innovation in teachers of the various faculties of San Martín National University. The study was of a correlational descriptive type. The sample consisted of 339 professors from the various faculties of the National University of San Martín. It is concluded that the use of technological tools in virtual education used by university teachers are: attendance, forum, grades, homework, etiquette, videoconference, polling, digital whiteboard, screen sharing and presenting videos, evidencing as a result, that the use of technological tools in virtual education is significantly related to educational innovation in professors of Peruvian public universities in the Amazon.