I'm going to assume you did not get the twist of the movie and will do my best to explain what happens:
The whole twist of the movie (and an excellent reason to watch it multiple times) is that The Narrator (nameless, some assume his name is Jack) actually has a split personality disorder. Tyler Durden does not exist and is just a figment of his split personality. It is explained when The Narrator sleeps, Tyler is awake. Any scene that involves either Tyler or The Narrator doing something, it is the same person doing it as he is both Tyler and The Narrator. What people actually see is The Narrator, whether it be Tyler's personality or not. Any scene involving the both of them is revealed to be The Narrator talking to himself or imagining themselves talking to one another.
With that bit of background out of the way, lets assume the fight with the van towards the end is just another one of their internal struggles. The two personalities fight over control of The Narrator's body and it seems that Tyler has won by throwing The Narrator down the steps, incapacitating The Narrator's personality, leaving Tyler in charge of the body. Therefore, when The Narrator regains 'consciousness' (so to speak), he realizes Tyler took them to the top of the skyscraper.
Hope that cleared it up.
In regards to the time, well, it is a very rare occurrence that 5 minutes is actually 5 real minutes. But the point that I haven't covered, that I realized, is the location that they're in. They are in a building, facing the one that was going to be blown up, for a better view. It is assumed that when The Narrator personality is 'knocked out', Tyler reset the charges and escaped to the top floor of the other building.