Would creating a digital card game with some mechanics that are similar to Yu-Gi-Oh violate some patents? Specifically, one shared mechanic is that the "field" or playing area is divided into 10 zones in 2 rows for each player, with "creature cards" placed in the front row, and other cards placed in the back row.
Well, I think that you are correct in worrying about Konami's intellectual property. As far as patents go, Konami has over 1100 patents on various gaming devices and methods. I imagine that some of them cover Yu-Gi-Oh!
I don't know which patents cover Yu-Gi-Oh!, but the patent numbers should be printed on the game or its container. If you do not see them there (they should be there), look at their website.
Aside from patents, you should also consider their trademarks (I presume that you are aware of the outcome of Konami's lawsuit against Upper Deck a few years ago).
I wish that I could have given you a better answer, but this is one of those instances that you will need to hire an attorney to guide you through the development process.
Good luck!
