Ansu Fati also scored as Barcelona overcame a slow start against its last-place opponent to open a five-point gap to Real Madrid ahead of the rival's home game against Valencia on Thursday.
Fati opened the scoring just before halftime and Messi converted a 69th-minute penalty for his league-leading 21st goal.
Also Read
Last time, when Barcelona played a home match without fans
The last time Barcelona played a home match without fans was in October 2017 amid the Catalonia separatist movement.
The team defeated Las Palmas 3-0 in a game played the same day of a controversial independence vote that the Spanish government deemed unconstitutional.
This time Barcelona was forced to keep fans away from the Camp Nou because of the pandemic, and the club placed banners and mosaics in the stands to honor those affected by virus.
La Liga points table: Barcelona at the top with 64 points
| La Liga points table | ||||||||
| Club | Matches played | Won | Draw | Lost | Goal for | Goal against | Goal difference | Points |
| Barcelona | 29 | 20 | 4 | 5 | 69 | 31 | 38 | 64 |
| Real Madrid | 28 | 17 | 8 | 3 | 52 | 20 | 32 | 59 |
| Sevilla | 29 | 14 | 9 | 6 | 42 | 0 | 12 | 51 |
| Real Sociedad | 28 | 14 | 5 | 9 | 46 | 34 | 12 | 47 |
| Getafe | 29 | 13 | 8 | 8 | 38 | 27 | 11 | 47 |
| Atletico Madrid | 28 | 11 | 13 | 4 | 32 | 22 | 10 | 46 |
| Villarreal | 29 | 13 | 5 | 11 | 46 | 38 | 8 | 44 |
| Valencia | 28 | 11 | 10 | 7 | 39 | 40 | -1 | 43 |
| Granada | 29 | 12 | 6 | 11 | 37 | 35 | 2 | 42 |
| Athletic Club | 28 | 9 | 11 | 8 | 30 | 24 | 6 | 38 |
| Osasuna | 28 | 8 | 11 | 9 | 35 | 39 | -4 | 35 |
| Levante | 29 | 10 | 5 | 14 | 34 | 42 | -8 | 35 |
| Real Betis | 29 | 8 | 10 | 11 | 40 | 47 | -7 | 34 |
| Valladolid | 28 | 7 | 11 | 10 | 25 | 34 | -9 | 32 |
| Alaves | 28 | 8 | 8 | 12 | 29 | 39 | -10 | 32 |
| Eibar | 28 | 7 | 6 | 15 | 28 | 44 | -16 | 27 |
| Celta Vigo | 28 | 5 | 11 | 12 | 22 | 35 | -13 | 26 |
| Mallorca | 29 | 7 | 4 | 18 | 28 | 49 | -21 | 25 |
| Espanyol | 29 | 5 | 9 | 15 | 25 | 46 | -21 | 24 |
| Leganes | 29 | 5 | 8 | 16 | 22 | 43 | -21 | 23 |
Videos of fans shown at Camp Nou
Videos sent by fans were shown at the stadium, and music by local violoncellists was played during the moment of silence observed before the match in memory of the victims of Covid-19.
Legans had the two best chances in the first 15 minutes one blocked by defender Clment Lenglet in front of the goal line and another denied by the post but Barcelona eventually took control and opened the scoring through Fati's low shot from inside the area in the 42nd.
WATCH: Barcelona vs Leganes full match
Click here to visit LaLiga facebook page
How Messi scored 629th goal for Barcelona
Messi's 629th goal for Barcelona came from the penalty spot after he was fouled following a run that started near the midfield line. He fired a left-foot shot into the corner to open a seven-goal gap to Madrid's Karim Benzema in the league's scoring chart.
Luis Surez returns
Luis Surez, who returned to action last week after recovering from knee surgery, came off the bench in the 54th to replace Fati.
Antoine Griezmann had a goal disallowed in the 64th after video review determined that Nelson Semedo was offside before making a cross to the French forward.
Barcelona next match
Barcelona visits third-place Sevilla on Friday.
La Liga: Other match results
In other results Tuesday, fifth-place Getafe drew 0-0 with Espanyol at home to remain winless after the break, while seventh-place Villarreal edged visiting Mallorca 1-0 for its second win in a row. Both Espanyol and Mallorca are in the relegation zone.
Espanyol played a man down from the 16th as Bernardo Espinosa was shown a straight red card for elbowing an opponent.
Mallorca had 15-year-old Luka Romero as an option on the bench for the first time, but the attacking midfielder born in Mexico from Argentine parents did not enter the match.
The youngster who is being dubbed by local media as the "new Messi" had a chance to become the youngest player to play in the Spanish league.
He is about a month younger than Francisco "Sansn" Bao Rodrguez was when he set the record by debuting with Celta Vigo in 1939-40.
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