The Argentine came into the match on 199 goals and reached his double century as he converted a penalty midway through the first half, before netting a fine second just before the interval.
Cesc Fabregas then added another and Messi rounded off the scoring right at the end with his second successive hat-trick to make it 202 goals in Barca colours - and 22 already this season.
"I am happy with the game, the result and to have got the 200 goals, but more than anything because of the result," the Argentine told TVE straight after the game.
"It was difficult because of the state of the pitch, because they pressed hard and committed fouls, but we did well."
Messi is now only 33 strikes behind Barca's all-time top goalscorer Cesar, who hit 235 between 1939 and 1955, but says the team is his only focus.
"It's not my objective [to pass Cesar's record]," he explained.
"I will just try and carry on helping the team to win and to score goals."
Messi's first goal for the Spanish giants came with a delicate lob after he was set up by Ronaldinho in a 2-0 win over Albacete in May of 2005, when he was just 17 years, 10 months and seven days old.
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