Batman is a boss. He creeps around in the shadows to take out the bad guys. He always has his handy-dandy utility belt. He doesn't use guns, he uses things like a Batarang, grappling hook, and smoke bombs. He has his fancy wing to help him fly off rooftops to arial attack his enemies. He serves justice to people like the Joker, Riddler, Scarecrow, etc. He stopped Bane from blowing up New York with a god forsaken nuke for Peanut's sake.
Batman would be smarter than that. he wouldn't sit there clueless. He would examine the situation and figure out how to stop the Flash. He could throw a smoke bomb, confuse the Flash, and come up with some solution to stop him. All it would take is to throw a rope out in the way of the Flash, tripping him, and then stopping him. The Flash couldn't stop him because he can run fast, not slow down time. Batman has all of his cool gadgets like his Batarang, Batmobile, and other bat vehicles. He has such a wide range of weapons to stop the Flash, while all the Flash has is his speed.
Batman could have stuck the Flash with a Bat-tracker, so Batman could be tracking him down with the Flash having no idea. He is running so fast, he could never tell. Batman would be on the way to intercept the Flash to stop him once and for all, and Flash would be clueless because he is running too fast to examine everything around him.