Section 16 states that a person shall be entitled to the credit of any input in respect of any supply of goods or services or both if:
a. He is in a position of tax invoice / Debit note issued by the supplier
b. He has in his position the goods or services or both
c. Tax charged in respect of such supply has been actually paid to the Govt
d. He has furnished the return u/s 39
Conclusion: You can treat the amount paid by you as input credit and utilise the same for subsequent payments if you have issued a credit note to the party (Condition a) and furnished the same in returns u/s 39 (condtion d)
[Since condition b and c are already satisfied ]