Face-to-face (or video) communication and demo
Not sure how you communicated your "queries on functionalties" to the stakeholders. It sounds waterfall-ish.
My question is how do I get the stakeholder to actually contribute
knowledge and participate in the agile processes?
Agile encourages face-to-face communication. Did you meet with the stakeholders? If your client is not in the same location as you are, get them on a video call. Nowadays with Google Hangout, Skype and other tools, this should not be difficult.
Also, one of the Agile principles is to "Deliver working software frequently". Even if you don't actually deliver the software, at a minimum you should set up a sprint review meeting and demo the working software to stakeholders. During the demo you can pause at the appropriate places and seek feedback and clarifications.
I worked with a client with similar challenges. Clients have other priorities and may not know your timeline. We initiated a practice to send out such requests with our expected response times. In a two week sprint you do not have much wiggle room. If the response is not received in a day or two then it becomes an impediment reported to the Scrum Master. The Scrum Master will follow-up, meet in person or escalate to senior levels - whatever it takes to get a response. It should become a crisis by the end of that sprint rather than get carried forward to the end of the project.