In fact, alif ا does not mean anything particular and that differs it from the rest of the Arabic letters. It is a kind of a service letter, now it is a support for hamza, now it is written as a horizontal line as in alif maddah آ, now it looks like a dotless yā’ ى, alif maqṣūrah, now it is not written at all (although it should have been there) as in ذٰلِكَ (ḏālika) “that”. So what is the function of the alif in the verb-final sequence وا? The short answer is:
In those verb forms the silent alif means those are 2nd and 3rd person plural masculine verb forms, but not nouns, not any other verb forms.
Note that the word-final sequence وا is found not only in the active voice perfect indicative 3rd person plural masculine form you mentioned, فَعَلُوا faʿalū “they (masc.) do”, but also in the subjunctive 2nd p. pl. masc. (تَفْعَلُوا tafʿalū “that they (masc.) do”) and 3rd p. pl. masc. (يَفْعَلُوا yafʿalū “may they (masc.) do!”), as well as in the same forms of the jussive mood — 5 forms in the active voice, and all those forms in the passive voice — 5 more forms, and the imperative 2nd p. pl. masc. – (اِفْعَلُوا ifʿalū “[you men,] do!”) — total 11 different forms of the Arabic verb ending in the sequence وا which is a sign there is a function in that alif, it is there not accidentally.
Also, the final وا in the perf. ind. 3rd p. pl. masc. is not always pronounced [u:] (oo). In the weak verbs that have wāw و as the 3rd letter of the root, e.g. ت ل و (t-l-w) تَلَا (talā) “to follow”, the final وا is read as [aw]: تَلَوْا (talaw) “they followed”. That is the first sign you could have noticed that the function of alif in this verb form is not connected with representing vowel sounds.
Let's take another triconsonantal root with the final wāw و — the root غ ز و (ḡ-z-w) with the general meaning of desiring, attacking, overcoming, and waging war. The noun formed from this root is غزو (ḡazw) “goal, invasion, disarray”, the verb is غَزَا (ḡazā) “to invade, to overcome” whose active voice perfect indicative 3rd p. pl. masc. form is غزوا (ḡazaw) “they invaded”. Compare:
غزو (ḡazw) “invasion”
غزوا (ḡazaw) “they invaded”
The only thing that distinguishes the two written words is the presence of the alif in the verbal form.
The verbs without the wāw و as the 3rd root letter don't end in ū [u:] in the singular, but it is not so with the final wāw و weak verbs, the same غَزَا (ḡazā) “to invade, to overcome”, let us see:
اغزو (ʾaḡzū) “I invade” (present indicative 1st p. sg.)
اغزوا (uḡzū) “invade!” (imperative 2nd p. pl. masc.)
يغزو (yaḡzū) “he invades” (present indicative 3rd p. sg. masc.)
يغزوا (yaḡzū) “that they invade” (present subjunctive 3rd p. pl. masc.)
يغزوا (yaḡzū) “may they invade!” (present jussive 3rd p. pl. masc.)
As you can see, it is only the presence of the otherwise senseless silent alif that tells the plural forms from the singular ones.
Of all the Arabic letters alif has the greatest number of functions. One of them is being a mere silent spelling convention for telling verbs from nouns and plural verb forms from the singular forms when the words are written without vowel diacritics.