If you are in a linux/unix environment you could use sed like such:

cat tmp.map | while read old new
do
  sed "s/$old/$new/g" tmp.gff > tmp2.gff
  mv tmp2.gff tmp.gff
done

Just make sure you keep a copy of your original gff file because this code over-writes the file. The $old will be the value in the first column and the $new is the value in the second. This loops through each line of your map file in turn to do the replacement. However, this is naive and will replace, for example, all 12's in the file to B1--including any coordinates etc. Below I've added some pre and post file processing using the awk command to eliminate this issue and only do the replacement in column 9. You can edit to include other columns if you need to:

#print column 9 to a file by itself 
awk '{print $9}' tmp.gff > col9.txt 

#print all other columns to a separate file 
awk '{print $1,$2,$3,$4,$5,$6,$7,$8}' tmp.gff > other.txt 

#run the replacement on column 9 
cat tmp.map | while read old new 
do 
  sed "s/$old/$new/g" col9.txt > tmp.txt 
  mv tmp.txt col9.txt 
done 

#paste the files back together 
paste other.txt col9.txt > final.gff

This is a little python script that will do the job.

gff_file = 'gff.txt'
map_file = 'map.txt'
out_file = 'output.txt'

my_map = dict()
with open(map_file, 'r') as f:
    for line in f:
        data = line.split('\t')
        my_map.update({data[0]:data[1]})

with open(out_file, 'w') as out:
    with open(gff_file, 'r') as f:

        for line in f:

            data = line.split('\t')

            for key, value in my_map.items():
                if key in data[-1]:
                    print(key,value)
                    print(data[-1])
                    data[-1] = data[-1].replace(key, value.strip())
                    print(data[-1])



            for item in data:
                out.write(item+'\t')