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the documentation actually states that 45 is the limit for the number of columns when using the data upload wizard. That being said, the wizard is not the only method for loading data to the database. You could load the data simply as a file and then post process that file, now a lob, into the desired table/s. Also, if you have access to the database server OS, you could load the file as an external table, with the process controlled from Apex.
To add to Vite DBA post, the limitation of 45 columns have been reported before and we are considering to have this extended in our coming release. Meanhwile there are couple of options you can use to upload your file as described above by Vite DBA. Here are two threads that explain well each of the method (using external table or loading the table and writing your own post-process)
Import data in excel to database table
Re: Upload data from csv to table in Apex