Clad in an Argentina shirt with Messi's number 10 on the back and holding his phone, the fan calmly walked onto the pitch in the 52nd minute and approached Barca defender Jordi Alba before heading towards Messi.
The intruder was tackled by security guards before he could make any contact with the six-times world player of the year, while two police officers helped remove him from the pitch.
La Liga leaders Barcelona won the match 4-0, with Messi scoring one goal and settingh up two others. Luis Suarez also made his first appearance since injuring his knee six months ago, coming off the bench in the second half.
The fan later told Spanish radio station Cadena Cope he was a French national living in Mallorca and that he had scaled a two-metre fence to enter the stadium shortly before halftime.
"I had planned this ever since I knew the match was happening, I wanted a photo with Messi and to meet him because he's my idol," he said, declining to give his name.
"I got a photo but it wasn't a very good one and the police made me delete it. I stopped with Jordi Alba to tell him I was going for Messi. It was a nice experience."
Only 229 people are allowed to enter stadiums for matches from now until the end of the season under the league's latest protocol on resuming the campaign.
The protocol also includes strict guidelines on how teams enter and leave stadiums for matches and obliges players to wear masks and gloves on the way from their team hotel to the ground as well as in the dressing room, among other rules.