The Argentine struck just before half-time to break yet another record and give the Catalans hope in the process after they had gone two behind and seen Adriano sent off
The Argentine curled home a stunning free kick just before half-time to level the scores on aggregate at 4-4, although Real Madrid have the advantage after netting two away goals in the first match at Camp Nou, which ended 3-2.
Messi's strike sees him overtake the previous Barcelona mark, set by Cesar Rodriguez. The 25-year-old also surpassed the forward's club record of 232 strikes last season.
Fellow Argentine Alfredo Di Stefano, who starred for Madrid in the 1960s, holds the overall record with 18 Clasico goals to his name.