While running from rooftop to rooftop, you will see an Agent drop down onto another roof across a gap. If you Focus and unload on him while running at him, he will start to dodge your shots. Jump across the gap and over the Agent, firing at him as much as possible. When you are over his head, stop Focusing. You will land behind him and although you will not be shooting at him anymore, he will still be dodging for a couple seconds. Use this opportunity to get in a good strong kick or try to knock him into the gap. If you do not get him in the gap on your first try, you should most likely quit. If you knock him off the roof, you will see his gun appear on the ground, then immediately shrink into nothingness. You have now defeated the Agent.
This isn't easy to do and may take some time. After seeing the first Agent, keep running as usual. When you reach the place where the agent jumps through the wooden roof, shoot at him to keep him occupied (or throw him in Focus mode). Run up the steps right away and let him follow you. When he runs at you, move out of his way and let him stand near the edge. Run up to him (not in Focus) and try to throw him. Eventually, he will fall off the edge. When he does, stand on the edge on one of the small "bars". When you look down, you will see Agent Smith laying down on the sidewalk with his gun beside him. Note: When you look down there, you will also see regular cops shooting at you.