I figured out a solution based on the following stackoverflow answer. For the prediction phase, you can use the tf.contrib.framework.load_variable to retrieve the embedding variable from a trained and saved Tensorflow model as follows:
if mode == tf.estimator.ModeKeys.PREDICT:
embeddings = tf.constant(tf.contrib.framework.load_variable('.','embed/embeddings'))
helper = tf.contrib.seq2seq.GreedyEmbeddingHelper(embedding=embeddings,
start_tokens=tf.fill([batch_size], 1),end_token=0)
So in my case, I was running the code from the same folder containing the saved model, and my variable name was 'embed/embedding'. Note that this only works with embeddings trained via a tensorflow model. Otherwise, refer to the answer linked above.
To find the variable name using the estimator API, you can use the method get_variable_names() to get a list of all the variable names saved in the graph.