Single word for the thing substituted

Agree with Mark Hubbard's comment. How about originals?

OD:

original: Present or existing from the beginning; first or earliest.

Your example:

These substitutions are not perfect. There are material differences between the substitutes and the originals.

These substitutions are not perfect. There are material differences between the substitutes and the substituted.

Here, the substituted stands (as a noun) for the things which were substituted. It is the past participle of substitute and hence functions as an adjective (as per the ODO definition of past participle), which in turn is allowed to act as a noun (in this context). Check the reference below, specifically, the example where the insured (past participle of insure) is used in the sense of those who are insured (noun).

M-W Learner's Dictionary - "Ask the Editor":

Adjectives used as nouns

Can adjectives function like nouns?
Answer: Just as nouns can function like adjectives, as we highlighted in our previous post, so can adjectives function like nouns.

A lot of adjectives are used this way, many referring to classes of people:
a shelter for the homeless
tax breaks for the insured