Bulk Insert Operations are your friend(s).
If it's a straight insert only (new data only in files) simply bulk insert the data directly to the table. Most databases have utilities to do bulk insert operations, some even expose those libraries to code as well if using command line utilities and batch files seem old fashioned.
If it's an insert/update/delete type of scenario, bulk insert into a staging table and then use RDMS specific technology to update the target table.
For example, SQL Server provides a nice MERGE command to merge data to a target.
Bulk inserting 100,000 records will only take a second or so. If your in the insert/update/delete scenario it will take a few more seconds to merge the data from the staging table to the main table.
With this approach you will be able to meet the 5 minute window.
If there is really this amount of data coming in every 5 minutes, then you will need data partitioning strategy as well to help manage the data in the database.
60/5 = 12 * 24 = 288
288*100,000 = 28,800,000 ~29 million records a day. 870 million records per month.
I would develop an archiving/purge strategy as well.