2.2 Payment for the performed works shall be made by Customer upon its performance on the basis of the certificate of acceptance of performed works and invoice of Contractor within 45 calendar days since the date of signing the certificate of acceptance of performed works.

on the basis of against the certificate of acceptance

Это русское построение фразы.

for the work performed

или for completed work (если использовать эту конструкцию)

Насчет ITS - можно (даже нужно) как-то по-другому, например:

The Customer shall pay for completed work on the basis of акта сдачи – приемки выполненных работ

Избегайте повторения в английском яз. русскоязычных бредней ("по факту их выполнения" и пр.)

invoice of Contractor = the Contractor's invoice

их not = to "its"
it's "thereof"

invoice of Contractor within - Contractor's invoice issued within или invoice issued by the Contractor

и артикли у вас вообще чего-то.

since - from/after, на худой конец of

отвечая на ваш вопрос: конкретные обоснованные замечания к такому переводу возникнут.

'выполненных работ ...... по факту их выполнения = 'the work [singular] carried out ...... upon its completion'

вариант от Google
2.2 Payment for work performed made by the Customer upon their performance on the basis of the certificate of delivery - acceptance of work performed and the invoice of the Contractor within 45 calendar days from the date of signing the act of acceptance - acceptance of work performed.

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Вопрос: Гугл научился переводить договора? Или где то есть подвох?

You can put it in the plural -- but 'works' [in the plural] usually means:
* завод; or
* the creations of a musician/writer/artist, eg 'the works of Beethoven'.

Thanks a lot, very detailed and clear! Are you a native speaker?