Will i be penalized for not filing my IT return physically although i have filed it through e filing in time?

No. The IRS prefers E-filing. It is easier on them.

I have been E-filing for years.

If you e-file your return with Digital Signature the date of e-filing will be considered as date of return filing, But if e-filing was without Digital Signature you are required to submit ITR-V physically and the date on which you submit ITR V will be considered as the date of return filing. If you file return without digital signature and yet not submitted ITR-V, this is equivilent to non submission of return.

If you submit your Income Tax Return online with digital signature, then you need not to submit it again in paper/physical format.

Otherwise you have to submit your Income Tax Return in paper/physical format with your signature.

I am sure there is time limit for submission of paper/physical format Return after the online submission. But unfortunately, I can't remember now. Most probably within 15 days after submission of online return.

when u file an income tax return on line without digital signatures u have to send a copy of the e return to income tax department. if u dont do so the return u filed on net will not be considered. u will have to pay a penanlty as if u have not filed a return.
this is valid in India only, for Indian citizens. of u are not a indian citizen then my reply has no meaning at all