Yes you will.
The ax authorities will consider the amount you paid for 1) the period of residence in Switzerland and 2) for the determination of the annual income and related deduction (tax rate determination).
Example1
- Salary from June to December 60 CHFK and 5 CHKF paid in the pillar A
60’000 120’000
-5’000 -5’000
55’000 at the rate of 115’000
- Salary from June to December 60 CHFK and 6.8 CHKF paid in the pillar A
60’000 120’000
-6’800 -6’800
53’200 at the rate of 113’200
The above applies for someone filling a tax return in Switzerland or asking for the benefit of the 3A when taxed at source until 31.12.2020.
From 01.01.2021, the law will change for people tax at source. A tax return will be needed to request the 3A deduction (same will apply for repurchase in the pillar 2).
Source - https://www.bdo.ch/fr-ch/publications/articles/nl/revision-de-l-imposition-a-la-source-2021