A video content matching system includes a computing platform having a hardware processor and a memory storing a software code. When executed, the software code obtains a reference digital profile of a reference video segment, obtains a target digital profile of target video content, and compares the reference and target digital profiles to detect a candidate video segment of the target video content for matching to the reference video segment. The software code also frame aligns reference video frames of the reference video segment with corresponding candidate video frames of the candidate video segment to provide frame aligned video frame pairs, pixel aligns the frame aligned video frame pairs to produce frame and pixel aligned video frame pairs, and identifies, using the frame and pixel aligned video frame pairs, the candidate video segment as a matching video segment or a non-matching video segment for the reference video segment.