Recent advances in cloud systems, on-demand circuits and software-defined networking have created new opportunities to enable complex, data-intensive scientific applications to run on dynamic networked cloud infrastructures. In this work, we present an end-to-end framework for autonomic adaptation for scientific workflows on networked cloud systems, which leverages novel network provisioning technologies. We present an application-independent controller framework called Mobius++ that includes dynamic network adaptation capabilities using Software-Defined Networking (SDN) mechanisms, which enables workflow management systems to address competing priorities of workflow operations, data movements in particular. We use a representative, data-intensive bioinformatics workflow as a driving use case to showcase the above capabilities. Experimental results show that the Mobius++ framework, in conjunction with a novel virtual Software Defined Exchange (SDX) platform, is able to dynamically prioritize bandwidths between different end-points, on-demand, and being driven by priority directives from a workflow management system. We show that data transfer jobs from two workflows with different priorities are accurately arbitrated as the relative priorities change.