Bash + coreutils, 29 bytes

date -d@${1::-3} +%y%m%d.%H%M

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JavaScript (ES6), 65 bytes

n=>'101010.1010'.replace(i=/d/g,x=>new Date(n).toJSON()[i=x-~i])

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How?

We initialize the pointer $i$ to a non-numeric value (coerced to $0$) and then add alternately $2$ and $1$ to it to pick the relevant characters from the ISO-8601 conversion of the input timestamp.

yyyy-mm-ddThh:mm:ss.sssZ

  ^^ ^^ ^^ ^^ ^^

JavaScript (ES6), 66 bytes

n=>'235689.BCEF'.replace(/w/g,x=>new Date(n).toJSON()[+`0x${x}`])

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How?

Once the input timestamp is converted in ISO-8601 format, all required characters can be accessed with a single hexadecimal digit.

yyyy-mm-ddThh:mm:ss.sssZ

  ↓↓ ↓↓ ↓↓ ↓↓ ↓↓

0123456789ABCDEF

PHP, 40 32 31 bytes

-8 bytes thanks to Luis felipe
-1 byte thanks to Jo King

<?=date('ymd.hi',$argv[1]/1e3);

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Simple naive answer. PHP's date function takes a format string and an integer timestamp. Input from cli arguments, which is a string by default, then /1e3 because date expects second-precise timestamps. This also coerces the string to a number.

MATL, 28 bytes

Thanks to @skiilaa for a correction in the output format.

864e5/719529+'YYmmDD.HHMM'XO

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Explanation

MATL, like MATLAB, defines date/time numbers as the (possibly non-integer) number of days since time 00:00 of the reference "date" 0-Jan-0000.

Thus we take the input, divide it by 86400000 (number of milliseconds in one day), add 719529 (number of days from MATL's reference to UNIX reference), and convert to the desired format 'YYmmDD.HHMM'.

GNU AWK, 34 33 characters

$0=strftime("%y%m%d.%H%M",$0/1e3)

(strftime() is GNU extension, will not run in other AWK implementations.)

Thanks to:

• 
  Jo King for suggesting E-notation (-1 character)

Sampler run:

bash-4.4$ awk '$0=strftime("%y%m%d.%H%M",$0/1e3)' <<< 1547233866744

190111.2111

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Perl 6,  111 89  87 bytes

{~DateTime.new($_/Ⅿ,:formatter{"{(.year%Ⅽ,.month,.day).fmt('%02d','')}.{(.hour,.minute).fmt('%02d','')}"})}

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{TR/-//}o{S/..//}o{.yyyy-mm-dd~'.'~(.hour,.minute).fmt('%02d','')}o{DateTime.new($_/Ⅿ)}

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{TR/- //}o{S/..//}o{.yyyy-mm-dd~'.'~(.hour,.minute).fmt('%02d')}o{DateTime.new($_/Ⅿ)}

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Explanation:

The o infix operator takes two functions and creates a composite function. The rightmost one gets called first, and the one to the left gets called with its result.

Basically we use 4 block lambdas to generate a single lambda.

Which is not much different to how a WhateverCode lambda like * + * gets created.

Divide by 1000 and use that to create a DateTime object.

{DateTime.new($_/Ⅿ)} # Ⅿ is ROMAN NUMERAL ONE THOUSAND (3 bytes)

The result gets used by:

{

   .yyyy-mm-dd # 2019-01-11



   ~ '.' ~     # str concatenation with '.'



   ( .hour, .minute ).fmt('%02d') # add leading 0s (returns List)

}

That leaves us with a string like 2019-01-11.19 11

We need to remove the first two digits

{S/..//}

We also need to remove - and

{TR/- //}

C (gcc) (32-bit, little endian), 67 bytes

f(t,s)long long t;{t/=1e3;strftime(s,12,"%y%m%d.%H%M",gmtime(&t));}

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On an ILP64 platform, the following 55 byte version should work:

f(t,s){t/=1e3;strftime(s,12,"%y%m%d.%H%M",gmtime(&t));}

PowerShell, 59 58 bytes

"{0:yyMMdd.HHmm}"-f(Date 1/1/1970).AddSeconds("$args"/1e3)

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Gets the Date of 1/1/1970 (defaults to 00:00:00am), then Adds the appropriate number of Seconds. Passes that to the -format operator, which correctly formats the datetime.

Probably culture-dependent. This works on TIO, which is en-us.

-1 byte thanks to shaggy.

Python 2, 64 bytes

lambda s:strftime('%y%m%d.%H%M',gmtime(s/1e3))

from time import*

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The input is considered to be in UTC.

Perl 6, 57 50 bytes

{TR:d/T:-/./}o{substr ~DateTime.new($_/1e3): 2,15}

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Takes the default stringification of a Datetime, in the format yyyy-mm-ddThh:mm:ssZ and modifies it to fit the output format. Perl 6 is in need of a date formatter method.

Explanation:

                       Datetime.new($_/1e3) # Create a date time

                      ~                 # Stringify it to the format yyyy-mm-ddThh:mm:ssZ

                                        # e.g. 2019-01-11T19:11:06.744000Z

               substr                      : 2,15  # Take the middle 15 characters

 {TR:d/T  /./}o   # Then replace 'T' with '.'

        :-        # Then remove ':' and '-'

C# (Visual C# Interactive Compiler), 67 61 60 bytes

n=>$"{new DateTime(1970,1,1).AddTicks(n*10000):yyMMdd.HHmm}"

For reasons unknown to me, DateTime.UnixEpoch doesn't work.

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R, 58 56 bytes

format(as.POSIXct(scan()/1e3,,'1970-1-1'),'%y%m%d.%H%M')

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Javascript ES6, 76 66 bytes

x=>new Date(x).toJSON().slice(2,16).replace(/D/g,a=>a>'S'?'.':'')

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-10 bytes thanks to Shaggy!

x // timestamp

=>

new Date(x) // date object from timestamp

.toJSON() // same as .toISOString()

.slice(2,16) // cut off excess

.replace(/D/g, // match all non-digits

a // a is matched character

=>

a>'S'?'.' // if a is T (bigger than S is shorter) replace it with .

:''       // if it's not T, replace it with nothing

          // this way the dashes get removed and the dot gets put in the right place

) // end of replace

C (clang), 117 111 bytes

Thanks to @chux and @ceilingcat for the suggestions.

#import<time.h>

*l;f(long t){t/=1e3;printf("%02d%02d%02d.%02d%02d",5[l=gmtime(&t)]%100,l[4]+1,l[3],l[2],l[1]);}

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jq, 33 characters

(30 characters code + 3 characters command line option)

./1000|strftime("%y%m%d.%H%M")

Sample run:

bash-4.4$ jq -r './1000|strftime("%y%m%d.%H%M")' <<< 1547233866744

190111.1911

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ksh, 36 bytes

printf "%(%y%m%d.%H%M)T" $(($1/1e3))

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Thanks to Jo King for 15 bytes saved

MediaWiki, 46 bytes

{{#time:ymd.Hi|@{{#expr:floor({{{1}}}/1e3)}}}}

Twig, 25 characters

{{d[:-3]|date('ymd.hi')}}

This is a template. Call it by including it and pass the Unix time as parameter d.

Sample usage:

{{include('datetime.twig', {'d': 1547233866744})}}

Try it on TwigFiddle