I presume you mean a proprietary license. Probably yes, you just have to obey the license. The Linux kernel and git are also GPL. In general, if you're not linking it into your software you're fine, but see the license for details.

Under US law at least, open source software is commercial: https://dwheeler.com/essays/commercial-floss.html

Pandoc is licensed under the GPL version 2 or later. I know of a couple of companies where pandoc is used in proprietary systems server-side. IANAL, so best to consult one for your specific use case.