The Argentine bagged two goals - one from a penalty, one from a rebound following his saved spot-kick - as the Blaugrana sealed an important win in the title race
The Argentine opened the scoring from the spot and struck his side's third from a rebound after his late penalty was saved by Adan, after Barca had been made to handle a nervy second period following Ruben Castro's goal.
The Catalan giants were in the headlines for all the wrong reasons this week after Fifa hit them with a transfer embargo for next season due to irregularities found in their dealings at youth level.
It will have come as an unwelcome distraction for Gerardo Martino and his men, who have plenty on their plate in a three-way fight for the title with Atletico and Real Madrid.
After Atletico's 1-0 win over Villarreal earlier on Saturday, Barca knew they could ill afford a slip-up against the league's bottom club and their nerves were settled when Messi rolled in a 15th-minute penalty.
A Jordi Figueras own goal midway through the second half gave the hosts some breathing space and, although Betis replied instantly through substitute Castro, Messi converted the rebound after another penalty was saved for his 25th league goal of the season.
The hosts, who remain within a point of Atletico, were rarely threatened by their beleaguered visitors, whose 3-1 win at Levante in their previous away outing was their first on their travels in the league all season.
Defeat leaves them nine points from safety with only six matches remaining, and the situation could yet get worse for Gabriel Calderon's side with three of the four teams immediately above them set to play on Sunday.
Xavi was first to threaten in the 10th minute, thumping an effort from the edge of the area, but Antonio Adan reacted brilliantly to get down low to his left and parry away.
It took Barca just five more minutes to move in front, Messi tucking away the penalty after Alexis Sanchez's twisting and turning inside the area had drawn a foul from Figueras.
The Argentinian went close to doubling his tally four minutes before the interval, jinking into space on the edge of the box before curling his shot narrowly wide of the left-hand upright.
Xavi almost added a second six minutes into the second half, but the midfielder's free kick from 25 yards glanced the top of the crossbar with Adan rooted to the spot.
Alfred N'Diaye gave Barca a rare fright in the 64th minute as Jose Manuel Pinto leapt to tip the midfielder's deflected effort over the top.
Three minutes later however, Barca surged further ahead in bizarre fashion.
Figueras was the unlucky man once more, diverting the ball into his own net as he stretched to cut out Adriano's pass towards Pedro.
The visitors showed some spirit in responding immediately, Castro picking up N'Diaye's cut-back and firing low beyond Pinto.
Hopes of a comeback were dashed four minutes from time, Messi just squeezing home the rebound after seeing his spot-kick saved by Adan when Juanfran was adjudged to have handled Neymar's cross inside the area.