Scientific knowledge is evolving at an unprecedented rate of speed, with new concepts constantly being introduced from millions of academic articles published every month. In this paper, we introduce a self-supervised end-to-end system, SciConceptMiner, for the automatic capture of emerging scientific concepts from both independent knowledge sources (semi-structured data) and academic publications (unstructured documents). First, we adopt a BERT-based sequence labeling model to predict candidate concept phrases with self-supervision data. Then, we incorporate rich Web content for synonym detection and concept selection via a web search API. This two-stage approach achieves highly accurate (94.7%) concept identification with more than 740K scientific concepts. These concepts are deployed in the Microsoft Academic production system and are the backbone for its semantic search capability.