Shibuya to Kyoto

Im travelling from Shibuya to Kyoto and via hyperdia the fair cost is a total of 13,910 yen. It says to travel the JR Yamanote line from Shibuya to Shinagawa and then transfer to the Shinkansen to go to Kyoto. The total train fare consists of the basic fare and the supplementary fare. Will I get 1 ticket for the basic fare and 1 ticket for the supplementary fare? Or will they be combined into 1 ticket? if they are two separate tickets, which ticket do I use to pass through the ticket gates at Shibuya to access the JR Yamanote line? And to access the Shinkansen line from Shinagawa do I put both tickets together at the same time through the ticket gate? (read from another article)

Thanks!!

Will I get 1 ticket for the basic fare and 1 ticket for the supplementary fare?

I have still not figured that out completely when city centers are involved. I think there is a chance that the two get combined into a single ticket in this case.

if they are two separate tickets, which ticket do I use to pass through the ticket gates at Shibuya to access the JR Yamanote line?

The base fare ticket.

And to access the Shinkansen line from Shinagawa do I put both tickets together at the same time through the ticket gate?

Yes, you put them both into the machine at the same time together.

Is your final destination located in Kyoto City?

I think there is a chance that the two get combined into a single ticket in this case.

I agree.

Maybe your JR basic-fare ticket and your Shinkansen (super-express) ticket are combined, maybe they are separate.

Anyway, I suppose you are highly likely to get issued a JR basic-fare ticket to travel from a station in Tokyo Ward Area [Tokyo tokunai] to a station in Kyoto City Zone [Kyoto shinai], as a single basic-fare ticket / with a Shinkansen ticket combined.
Traveling with this ticket, you are not allowed to make a stopover outside the exit gate(s) at a station in Tokyo Ward Area (e.g. Shinagawa in your case) or at a station in Kyoto City Zone.

In Shibuya Station, you put the single basic-fare ticket / the combined ticket through a gate machine at an entrance gate.
Trains (for Shinagawa) on the Yamanote Line's inner loop depart at Track 2 in Shibuya Station; please note that trains destined to Osaki do not run to Shinagawa.

In Shinagawa Station, you put the both tickets / the combined ticket through a gate machine at either Shinkansen South Transfer Gate or Shinkansen North Transfer Gate.
http://english.jr-central.co.jp/info/station/_img/shinagawa_L.jpg
Westbound Shinkansen trains depart at Track 23 or 24 in Shinagawa Station.

In Kyoto Station
http://english.jr-central.co.jp/info/station/_img/kyoto_L.jpg
: If you pass through a Shinkansen transfer gate first and an exit gate second,
at the transfer gate the single basic-fare ticket is returned while the Shinkansen ticket is collected / the combined ticket is returned,
and then at the exit gate the single basic-fare ticket / the combined ticket is collected.
: If you pass through a Shinkansen gate other than transfer gates,
that gate works as an exit gate, and a gate machine collects the both tickets / the combined ticket there.

Thank you guys so much!!

@omotenashi
How would I know if the JR Yamanote Inner loop will stop at shinagawa or just finish at osaki?
Im kind of confused, Hyperdia says to take the JR Yamanote Line Inner loop which stops at osaki and then shinagawa, but it doesn't say transfer? Does the train just continue on to Shinagawa?

DEPART: SHIBUYA (JR Yamanote Line Inner Loop for OSAKI) ---
OSAKI (JR Yamanote Line inner Loop for OSAKI) ---
TRANSFER: SHINAGAWA (Shinkansen) ---
ARRIVE: KYOTO

If you type in Hyperdia Shibuya to Kyoto (I did July and around 12pm), you can see that there is a stop at OSAKI

Schedules for July are not yet available, do not use Hyperdia to plan trips after April 30. If you take the Yamanote line, there is no transfer at Osaki. There is one if you take some other line from Shibuya to Osaki.

If you take the Yamanote line, there is no transfer at Osaki.

Actually a passenger may have to change trains even on the Yamanote Line.
While most trains in operation on the Yamanote Line run in circles, there are also some trains which go to one destination, beyond which they become out of service.

When the first train on the inner loop which you can take from Shibuya Station goes only to Osaki, usually you can ignore it and catch a train which runs in circles within several minutes (except during very late hours).

Does the train just continue on to Shinagawa?

Yes.
In the HyperDia result, you probably see this icon at Osaki, which means that the train continues on the next section, i.e. you don't have to change trains at this station.
http://www.hyperdia.com/en/images/icon_choku.gif

How would I know if the JR Yamanote Inner loop will stop at Shinagawa or just finish at Osaki?

You can tell it by signs like "Bound for Shinagawa & Tokyo" or "For Osaki" on LED boards on the train's body.

Because expressions like "inner" or "outer" are often not passenger-friendly, the direction in which a Yamanote Line train (which runs circularly) goes is sometimes indicated by the nearest two among the following six stations: Shinagawa, Tokyo, Ueno, Ikebukuro, Shinjuku and Shibuya.

I did July and around 12 pm

JR companies will revise timetables on 26 March 2016.
In this revision, trains on the Yamanote Line will probably remain the same, while Shinkansen Nozomi trains will be rescheduled.

HyperDia seemed to be late in reflecting new time data regarding past revisions of railroad timetables.
Hopefully JR-Central, which operates Tokaido Shinkansen connecting Tokyo and Shin-Osaka, may upload the new timetable on its website by the end of February.

While it is unlikely to impact on this particular journey, Osaki is the "terminal station" on the Yamanote line. I've been on trains that finish there and needed to get on a different service.

@ JapanCustomTours

You don't understand "Osaki stop" real meanings.
https://www.youtube.com/watch?v=uV2JlerRNlg
http://loo-ool.com/rail/e233.cgi?guid=ON&a=Y,0,,,0
During weekday morning rush about 60 full trains running as peak.
(evening rush is fewer about 40 trains running)
But other time no need such too much amount trains.

Operate No.1G means round and round 19 times/day on only outer loop
from early morning to midnight as No break/back to yard train.

So just you took back for yard train.

it is a loop.
don't worry about a mistake. if you fail to get off at the station, just take off and get a reverse train to go back.
most trains run in a loop continuously.
some run out from a loop. some run into a loop.
all trains in Japan run in the left side, as cars run in the same side in japan. therefore, outer means clockwise, inner means counter-clockwise.