Why Is My Shinkansen Ticket So Cheap?

Today I bought a ticket for next Monday, to go with the shinkansen from Osaka to Yokohama, and the machine only wanted 5740 Yen from me.

But that's only the price of the seat. There's about 8000 Yen missing from the real ticket price, for the actual trip itself.

Surely this is going to slow me down on the day I want to board the train. What exactly happened here, and where, when and how do I pay the rest of the ticket?

That is because you only bought the shinkansen supplement (also known as limited express fee or “Á‹}Œ”). You did not purchase the base fare (�æŽÔŒ”), which is roughly another 8000 yen. You have to go to the ticket machine (or counter) once more and also purchase the base fare.

Here are some basics about tickets:
http://www.japan-guide.com/e/e2359_001.html

Did you check www.hyperdia.com before buying your ticket? you could have found the actual price...as long as you choose the right options..

By the way are you going from Osaka to Yokohama or from Shin-Osaka to Shin-Yokohama or any other combination?

For example from Osaka to Yokohama you will have to take a regular train or the subway from Osaka to Shin-Osaka, then the shinkansen to Shin-Yokohama then a regular train or the subway to Yokohama..

I went to the midori-no-madoguchi machine and bought a ticket from the Shin-Osaka to Shin-Yokohama.

I went to Hyperdia and looked at the real price. I knew what the real price was, which is why I made this post.

What I don't get it why you would have the option of buying just the seat at all. surely everybody who buys a seat would also like to go somewhere with the train.

What I don't get it why you would have the option of buying just the seat at all.

There are many cases in which a traveler prefers to buy the base fare ticket and shinkansen supplement separately. Probably the most frequent case is when you don't know the specific train yet for which you want to make a reservation along a multi-ride journey.

For example, if you make a journey from A via B to C, but don't know yet when you will take the train from B to C. Then you will buy first a base fare from A to C and a supplement from A to B, but you won't buy the supplement from B to C until later.

But it is true: in most of the cases, the base fare ticket and shinkansen supplement are purchased at the same time.

I bought a ticket for next Monday
I went to the midori-no-madoguchi machine and bought a ticket from the Shin-Osaka to Shin-Yokohama.
the machine only wanted 5740 Yen from me.
where, when and how do I pay the rest of the ticket?

It seems you mean "midori-no-kenbaiki" introduced on this page with a photo.
http://www.jr-odekake.net/railroad/midori/ticket/about.html

I suppose the best way is to visit a station early on the day and buy a base fare ticket, through a "midori-no-kenbaiki" machine or at a ticket counter.

: Most "midori-no-kenbaiki" machines in stations in Osaka Prefecture become ready by 06:40, some by 05:30 (e.g. those in Shin-Osaka Station and on the first [ground] floor of Osaka Station). One exception is a machine on the third floor of Osaka Station, which becomes ready at around 09:30.
: Probably you will get a base fare ticket valid from inside Osaka-City ("Osaka shinai") to inside Yokohama City ("Yokohama shinai").
: Before the scheduled time of departure, you can replace your Shinkansen ticket, with no special fee but only once, by another Shinkansen reserved-seat ticket if you hope. That means if you can get your base fare ticket too early for the train, you can try reservation for an earlier train.
: I don't recommend canceling your Shinkansen ticket on the previous day or later; because the departure is approaching, the cancelation fee is of 30 percent of the price, much higher than 320 yen for an earlier cancelation.

In principle, unless a Shinkansen ticket or another Ltd. Express ticket is purchased together, a base fare ticket cannot be sold in advance of the day of ride. Presumably you missed the option shown by the machine to buy your base fare ticket, and pressed the button to get issued a Shinkansen ticket only.

But that's only the price of the seat.
What I don't get it why you would have the option of buying just the seat at all. surely everybody who buys a seat would also like to go somewhere with the train.

To be precise, the 5740 yen charge is for taking a Shinkansen Nozomi train on a reserved seat, and the price of the seat is 1010 yen.
A passenger cannot replace a reserved-seat ticket by a non-reservation ticket, but can do vice versa by paying for the gap under the mentioned no-fee-but-once rule, even on the train if there is a vacant seat.

As Uji explains, there may be a case in which a passenger has a base fare ticket but does not have all the train tickets.
And, as to long-distance journeys it's often not the best choice to buy a base fare ticket each for the same section of the train ride.
Say an adult passenger plans to start from Shin-Osaka, get to Shin-Yokohama taking a Shinkansen train and stay around it for five nights, then move to Niigata on the sixth day changing Shinkansen trains at Tokyo. If base fare tickets are purchased for the three sections of the Shinkansen rides, the prices are 14130 yen in total. But it's better to buy one base fare ticket valid from inside Osaka City to Niigata Station, because the duration, which is six calendar days, is enough for the whole way and it's more cost-saving with the price of 11340 yen.