sudo systemd-resolve --flush-caches

Check the statistics in order to make sure that your cache size is now zero, thus cleared:

sudo systemd-resolve --statistics

returns:

DNSSEC supported by current servers: no
 
Transactions                
Current Transactions: 0     
  Total Transactions: 169902
 
Cache                       
  Current Cache Size: 39    
          Cache Hits: 162   
        Cache Misses: 190   
 
DNSSEC Verdicts             
              Secure: 0     
            Insecure: 0     
               Bogus: 0     
       Indeterminate: 0