You can dump the data to a temporary file, and them call the sqlite utility with a driver script that imports the temporary data file using an .import directive.

open my $temp, '>', $temp_filename or die ...;

for (@data) {
  print $temp join('|', ...), "\n";
}

open my $driver, '>', 'import.sql';
print $driver ".import $temp_filename\n";
...
system sqlite3 => -init => 'import.sql', $dbfile => '.quit';
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