The Oxford English Dictionary says of the word 'prayer':
'Monosyllabic pronunciations are suggested by metre from c1600, although disyllabic pronunciations are occasionally recorded in verse until at least the mid 17th cent.'
This particular phrase appears to be from a verse setting of a psalm, and in the original poem two syllables are required for 'prayer' in order for it to scan:
'Attend mine humble prayer Lord, with thine attentive eare, even in thy truth and justice Lord, vouchsafe my sute to heare'
(Ironically, 'even' has to be treated as a single syllable here.)
None of this necessarily means you have to sing it as two syllables in a modern performance, though. I suspect most English choirs would make it one syllable over two notes. But perhaps some specialist early-music choirs would use a two-syllable pronunciation.