Multiple Updates in MySQL

Yes, that's possible - you can use INSERT ... ON DUPLICATE KEY UPDATE.

Using your example:

INSERT INTO table (id,Col1,Col2) VALUES (1,1,1),(2,2,3),(3,9,3),(4,10,12)
ON DUPLICATE KEY UPDATE Col1=VALUES(Col1),Col2=VALUES(Col2);

Since you have dynamic values, you need to use an IF or CASE for the columns to be updated. It gets kinda ugly, but it should work.

Using your example, you could do it like:

UPDATE table SET Col1 = CASE id 
                          WHEN 1 THEN 1 
                          WHEN 2 THEN 2 
                          WHEN 4 THEN 10 
                          ELSE Col1 
                        END, 
                 Col2 = CASE id 
                          WHEN 3 THEN 3 
                          WHEN 4 THEN 12 
                          ELSE Col2 
                        END
             WHERE id IN (1, 2, 3, 4);