Topological Yang-Mills theory with the Belavin-Polyakov-Schwarz-Tyupkin SU(2) instanton is solved completely, revealing an underlying multi-link intersection theory. Link invariants are also shown to survive the coupling to a certain kind of matter (hyperinstantons). The physical relevance of topological field theory and its invariants is discussed. By embedding topological Yang-Mills theory into pure Yang-Mills theory. it is shown that the topological version TQFT of a quantum field theory QFT allows us to formulate consistently the perturbative expansion of QFT in the topologically nontrivial sectors. In particular, TQFT classifies the set of good measures over the instanton moduli space and solves the inconsistency problems of the previous approaches. The qualitatively new physical implications are pointed out. Link numbers in QCD are related to a non-Abelian analogue of the Aharonov-Bohm effect.