In english, this is what your code does. I've included comments where I think that you are mistaken about what your code is actually doing.

LOOP1: 
  1.0 Read one line of data from log file and store in 
      symbol $_
  2.0 Create an array of simple strings by splitting the 
      string stored in $_ wherever there is a comma.  Store 
      this array in @values.
      NOTE:  Each element of @values is a SINGLE string, 
             not an array.
  3.0 Connect to database
      NOTE:  This will connect you to the database
             everytime you read a line from your log
             file because it is inside the loop that
             reads your log file!
  LOOP2:
      3.1 Process each element of the array @values.  
      3.2 If this element is 'stop' then
          3.2.1 Create sql statement.  But you are
                using @values[0].  What does this mean?
                Each element of @values is a simple string.
                Did you only want that string, or did you
                expect that @values = ([array],[array]...)
                ???
          3.2.2 Preparing the sql statement.
          3.2.3 Bind parameters to $_->[i] ???
                But $_ is simply the single line of data that
                you read from your log file.  It's a single string!
                Why do you expect it to be an array?
          3.2.4 Execute db query
          3.2.5 Rollback if error
          3.2.6 Disconnect from database

... MISSING CODE....
      3.3 End of is current element of @values equal to 
          string 'stop'?
      3.4 Go back to LOOP2 to process more elements
          of the array @values (until all done)
  4.0 Go back to LOOP1 to read next line of LOG file
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I think you need to fix your algorithm first, then, once you have something that makes sense, convert it to perl.

At this stage, your algorithm is so mangled that it is not really a 'perl' problem. Perl is doing exactly what you are telling it to do, and then get's lost when you want an array from something that is not an array.