Madara was there to accomplish a 'mission'. Extract the kyuubi and get it under his control. When that was spoiled by Minato (who is like a God in Narutoverse) he had no reason to fight Minato anymore. Plus that Rasengan to the back wasn't enough to kill him now was that. He just suffered a damaged arm as I recall.
@hitsusatsu11: How was it a stalemate? He challenged Minato to combat and ate a rasengan to the back a minute later and had to retreat, allowing Minato to deal with the Kyuubi and prevent the destruction of the village. He's gotten massive upgrades but all his powers ever did were get him defeated in every fight that mattered. He's strong in plot because he's Madara, the ultimate baddie but what are his real feats in the series? Beating up some kid ninjas? Defeating Danzo's goons who couldn't even beat the Mizukage's cronies? Outside of brain washing the Mizukage (which helped him assemble of team of people who either quit on him, blew him in half, or got beaten up and killed by children.. ie things that are more fail than impressive), he's hasn't really done anything to live up to the legend.
Now you can't say that because he retreated he was defeated. It was more like a tactical retreat as I said earlier. Why would he fight Minato after his mission failed. As he said there were many doors left open for him to take control of the Kyuubi, so why would he try to compromise his chances. And I think Minato used his most powerful move ( minus death god consuming seal ) Hirashin level 2 and only gave him an injured arm. This very attack could have taken out (i.e. killed) almost anyone else in Narutoverse but Madara survived.
Plus if it were a full out battle, Madara could have easily used Izanagi ( I know it would cause him to loose his eye but he doesn't use them that much from the beginning) and continue the battle. And I don't think Madara would have fallen for the same trick twice and I think most of us can agree on that.