I am sure that it can be done in a more pythonic way, but I use a simple python script, which calls gdallocationinfo process and exports results to CSV (you must have GDAL installed). If you want to try, just copy the script below, fill in your sites list and path to your raster file.
import os
from subprocess import Popen,PIPE
import csv
sites= [
['Point1',-15.39495,28.33711],
['Point2',-15.548307,28.248216]
] ## 'Name',Lat,Lon
rast = '/path/to/raster/my_raster.tif'
param = 'Raster_VALUE'
csvoutfl = 'sites.csv'
##==
scr = open(csvoutfl, 'w')
header = 'site,lat,lon,{}'.format(",".join(param))
for i in sites:
csvline = '{},{},{}'.format(i[0],i[1],i[2])
result = os.popen("gdallocationinfo -wgs84 -valonly {0} {1} {2}".format(rast, i[2], i[1])).read()
try:
result = float(result)
except ValueError:
result = 'Err'
csvline += ',{}'.format(result)
scr.write('{}\n'.format(csvline))
scr.close()
print "\n\nCREATED: {}\n\n=== Finished ===".format(csvoutfl)