Barcelona's victory opened up a 15-point cushion over Real Madrid and Sevilla at the top of the Spanish league table. Numancia had defeated Barca 1-0 on the opening day of the season - their only league defeat of the whole campaign - and revenge was sweet as Barca stretched their unbeaten run to 19 games.
Messi grabbed a brace scoring the 49th minute opener and on 76 minutes to make it 14 goals for the season while Eto'o and Henry grabbed a goal apiece.
Eto'o now has 19 goals in as many games while Henry has 12 underlining Barca's potency in front of goal. It was a sombre mood in Barcelona after strong winds had ripped the roof off a sports centre in the city taking the lives of four children who had been inside preparing for a baseball game. The players paid a minute's respect for the victims before the kick-off.
Dani Alves almost put Barca in front after just five minutes when his cross deflected onto the crossbar. Numancia had lost nine out of their 10 away matches while Barca had the best home record in the division but it was the visitors who had the ball in the net first.
Javier del Pino rose highest to head past Victor Valdes but the goal was disallowed with Del Pino accused of climing on Andres Iniesta. At half-time it was a frustrating 0-0 for Barca but Alves set Messi up for an opener four minutes after the break and Eto'o showed great strength to add another four minutes later.
Jose Barkero got his side back in it with a brilliant free-kick but Henry and Messi wrapped up the game late on. Villarreal's Champions League hopes suffered a setback as they dropped two more points in a 1-1 home draw with lowly Osasuna on Saturday.
Giuseppe Rossi struck on 28 minutes to put Villarreal in front at El Madrigal and they looked set to climb to fourth in the table until Osasuna levelled through Eduardo Dady in the 64th minute.
It was a repeat of the 1-1 draw between the two sides in Pamplona and Villarreal stay fifth, four points behind Real Madrid and Sevilla who both have a game in hand. For Osasuna it was an important point in their survival battle. They have moved off the foot of the table at Real Mallorca's expense but are still six points from safety.