SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    13056, 13689, 13687, 13686, 13377, 12913, 
    12912, 13036, 12676, 12617, 12406, 
    12302, 12350, 12339, 12349, 12344, 
    12298, 18728, 18727, 12125
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00067

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 40 Using where

Result

product_id price
12125 1.69000000
12298 1.69000000
12302 1.69000000
12339 1.69000000
12344 1.69000000
12349 1.69000000
12350 1.69000000
12406 1.69000000
12617 1.69000000
12676 1.69000000
12912 1.69000000
12913 1.69000000
13036 1.69000000
13056 1.69000000
13377 1.69000000
13686 1.69000000
13687 1.69000000
13689 1.69000000
18727 1.69000000
18728 1.69000000