I'm thinking of Islamic counterparts to works by authors like Vegetius, Sun Tzu, Machiavelli, Clausewitz, Jomini, etc.
Sure, there are plenty. Unfortunately I can't read Persian so I haven't dealt with it first hand but Nizam al-Mulk was an incredibly powerful and intelligent Seljuk vizier who wrote extensively on politics and war: http://en.wikipedia.org/wiki/Siyasatnama
Ibn Khaldun, while perhaps less concerned with warfare directly was deeply concerned with the socio-economics of a state predicated upon war. He was particularly concerned with the cyclical dynastic workings of nomadic conquerers, given how often such tribal groups tended to rule large swathes of the middle east and central Asia. His most famous work is his Muqadimmah: http://en.wikipedia.org/wiki/Muqaddimah
There are good translations of it in English and it makes for compelling reading today. There's also a good In Our Time podcast on his life and work: http://www.bbc.co.uk/radio/player/b00qckbw
edit: ah, there is an English translation of Nizam al-Mulk here, now that I think about it I believe I've read extracts of it but don't think I've ever read the whole thing, obviously from amazon it's quite pricy. http://www.amazon.com/The-Book-Government-Rules-Kings/dp/0700712283/ref=sr_1_1?ie=UTF8&qid=1412886243&sr=8-1&keywords=nizam+al+mulk