I think this should work.
$date = "20/04/17 13:27:5";
$sec = substr($date, strrpos($date, ":") + 1);
$sec = substr("0{$sec}", -2);
$new = substr($date, 0, strrpos($date, ":") + 1) . $sec;
$newDate = Carbon::createFromFormat('d/m/y H:i:s', $new);
I changed the format since you were using m twice for "minutes" and "month". It is correct for the month, but not for the minutes. Instead use i for minutes with leading zeroes.
$sec Is what I used to get the second from the string. This gets the last position of : and will take everything after it. This assumes that you do not change the format of the string.
substr("0{$sec}", -2) Adds a zero to the current second and extracts the last two characters. That means that 50 becomes 050 and then the last two characters are 50 so we end up without the padding, but 5 becomes 05 and the last two characters are the only characters.
$new concatenates the start of the date string and the new second with the zero padding.
$newDate is your original string with the format changed.
H:m:stoH:i:sfor minutes