Can I get a Taiwanese visa being a Pakistani passport holder?

As stated in Timatic, the database used by airlines:

Visa required, except for Nationals of Pakistan can obtain an e-visa for a maximum stay of 30 days. The e-visa must have the remark "P, Special Permission from MOFA" and passengers do not require an invitation letter. Passengers must have a printed e-visa confirmation.

The e-visa can be applied for here. For Pakistanis, it is only issued "for the purpose of conducting business at the recommendation of local offices of the Taiwan External Trade Development Council (TAITRA)"

So ask your host to apply to the TAITRA for a recommendation through the Taiwanese Ministry of foreign affairs.

If they can't do that, you must apply for a regular visa, which you can do in Thailand as per this official document of the Taipei Economic and Cultural Office in Thailand. However, the same approval as for an e-visa may be necessary.

From your question I am assuming that you are a Pakistani citizen residing in Thailand interested in getting a visa for Taiwan.

Your best bet is to contact the Consular Divison of the Taipei Economic and Cultural Office in Thailand.

Contact information: 02-6700200 ext 342 (Visa for Aliens)

PS: The reason why I recommend this is because some countries need you to apply from your home country. I am absolutely not sure about Taiwan (Republic of China). e.g. (Not an example of your scenario but) I know people who aren't Pakistani citizens and needed to apply for a 'Hajj' visa while in Pakistan; and, the Saudi Embassy simply declined to accommodate them saying that the Embassy in Pakistan provides services to local citizens or Saudi citizens only.

Yes, you can get a visa for Taiwan but the approval needs to come from their ministry of foreign affairs. Once the visa is approved, you must print the confirmation before flying to Taipei.

source: timatic.