Commutative diagrams really show their significance when dealing with categories, so I would guess they first appeared in that context. Look at the paper which first introduced categories: Eilenberg and Mac Lane's "General Theory of Natural Equivalences" (Trans. AMS) 58 (1945), 231--294. You can find that paper through JSTOR, but if you don't have access to JSTOR then get it at killingbuddha.altervista.org/FILOSOFIA/GToNe.pdf. In this paper, commutative diagrams are used only a few times and the authors don't say the diagrams *commute*. Instead they use more elaborate descriptions like "the two paths around the diagram are equivalent". Even if this is not the first place a commutative diagram appeared, that they are used sparingly (considering the context) and described in an awkward way suggests it was one of the earliest times this concept jumped off the blackboard into print.

Weibel's paper on the history of homological algebra, which is available at his website, may provide some earlier sources if you track down references he gives.

EDIT: Perhaps the first book which made extensive use of commutative diagrams is Eilenberg and Steenrod's "Foundations of Algebraic Topology" (1952). On page xi they introduce that name.