There're couple of possibilities which completely not solved my problem yet.
First I tried to use PhoneGap but I can't use it anymore because of IndexedDB issues currently it has.
Then I switched to the option to call a native mobile application from a web page that can read a barcode.
Eventually this native application has to return barcode data it's read, in order to make use of it within web app.
I couldn't figure it out properly and appreciate if someone can explain this if it's possible. Some of the questions I looked at as of now;
Since commentator not answered even it's the real answer, I'm answering my own question to be shared openly.
Even it's possible to call another application to read barcode, it's not possible to turn back to the same app with this 3rd party app if it's not also managed by you directly.
So the alternatives may vary depending upon the specific situation but I had to let user make the 3rd party app to read barcode, and then wait user to turn back to my originated application after getting these results linked to my website.