To simply replace the value in (row,col) with a new value:
$ awk -F'|' -v OFS='|' -v row=2 -v col=3 -v val=corollacoupe 'NR==row {$col=val} 1' file 
#car|year|model
toyota|1998|corollacoupe
toyota|2006|yaris
opel|2001|corsa
This will set the value of input field col to val, but only in the input record row. The 1 in the end will ensure each record is printed by default. Input and output field separators are set via -F option and OFS variable.
If you need to make these changes in-place, create a temporary output file and then copy it over the original:
$ awk ... file >file.tmp && cp file{.tmp,}
Alternatively, in GNU awk, you can use the inplace library via -i inplace option:
$ awk -i inplace -F'|' -v OFS='|' -v row=2 -v col=3 -v val=corollacoupe 'NR==row {$col=val} 1' file 
If you wish to skip the comments, and count only non-comment rows:
$ awk -F'|' -v OFS='|' -v row=1 -v col=3 -v val=x '/^[^#]/ {nr++} nr==row {$col=val} 1' file 
#car|year|model
toyota|1998|x
toyota|2006|yaris
opel|2001|corsa