You have to distinguish between the yoga philosophy and the practice. The practice of yoga was and is accepted by all the schools of Vedanta. The philosophy of yoga differs little from the Samkhya philosophy. Swami Vivekananda writes in his Preface to his translation of Patanjali's Yoga Aphorisms (Complete Works, V1, sub-heading Raja Yoga, available here - http://www.advaitaashrama.org/cw/content.php):
All the orthodox systems of Indian philosophy have one goal in view, the liberation of the soul through perfection. The method is by Yoga. The word Yoga covers an immense ground, but both the Sânkhya and the Vedanta Schools point to Yoga in some form or other.
The subject of the present book is that form of Yoga known as Raja-Yoga. The aphorisms of Patanjali are the highest authority on Raja-Yoga, and form its textbook. The other philosophers, though occasionally differing from Patanjali in some philosophical points, have, as a rule, acceded to his method of practice a decided consent...
The system of Patanjali is based upon the system of the Sankhyas, the points of difference being very few. The two most important differences are, first, that Patanjali admits a Personal God in the form of a first teacher, while the only God the Sankhyas admit is a nearly perfected being, temporarily in charge of a cycle of creation. Second, the Yogis hold the mind to be equally all-pervading with the soul, or Purusha, and the Sankhyas do not.
You can read a more detailed description in Chandradhar Sharma's book A Critical Survey of Indian Philosophy (available here: https://archive.org/details/IndianPhilosophyACriticalSurvey) on pages 169-174. On page 174 he writes:
But God of Yoga is not the creator, preserver or destroyer of this world. He is only a special Purusa. He does not reward or punish the souls. Innumerable Purusas and Prakrti, all eternals and absolutes, are there to limit Him. He cannot grant liberation. He can only remove the obstacles in the upward progress of the devotees. Directly He has nothing to do with the bondage and liberation of the Purusas. Ignorance binds and discrimination between Prakrti and Purusa liberates. The end of human life is not the union with God, but only the separation of Purusa and Prakrti. Such a conception of God is certainly unsatisfactory.