I'm assuming that this is sorcerer Jafar and not genie Jafar. As that hardly seems like a fair fight as he has all kinds of reality warping fuckery on a near universal level at his disposal.
As a sorcerer Jafar can transmute objects [turned a Tiger into a kitten and an elephant into a monkey] levitate people and objects as large as a palace tower, sending it flying into the atmosphere. He can manipulate people to do his bidding like a puppet master. His spells seems to work instantly.
My concern is Jafar's speed and toughness. He certainly has the power to defeat Shepard with his spells, quite easily in fact, but Shepard has proven himself to be much faster than an average human, which is what Jafar fought. He didn't fight the Genie until he became a genie.
As a snake he certainly has the speed to keep up with Shepard, but Aladdin was able to harm him with a sword. Shepard has all kinds of crazy weapons at his disposal, some of which would do a lot more damage than a sword.
Shepard seems to have a few special abilities, one in particular is telekinesis where he can lift, pull, or throw objects. He also has the power to turn invisible for up to 6 seconds, create shock waves, and manipulate gravity.
With his special abilities and speed combined with his weapons he could feasibly be able to counter sorcerer Jafar's spells and defeat him. I'm not totally sure though. I'm still on the fence to be honest.