Vargas, 24, gets the call up from New Orleans, taking the rotation spot of the recently demoted Mike Pelfrey. The lefty was the centerpiece of an offseason trade that sent relievers Matt Lindstrom and Henry Owens to the Marlins.
Vargas went 2-3 with a 5.30 ERA in seven starts for New Orleans, after going 1-1 with a 2.25 ERA in eight innings this spring.
"I've seen Vargas before, and I like his stuff," said Mets manager Willie Randolph. "When we first made the move, I kind of liked the move at the time. Obviously, he didn't make the club out of Spring Training, but I thought it was nice to have him as a backup down there."
Vargas was 6-7 in two Major League seasons with the Marlins, posting a 5.25 ERA but walking 61 batters in just over 116 innings.
"He's young, he's athletic," Randolph said. "He can swing the bat a little bit -- I like guys who can handle their position -- and he's got a taste of the big leagues."
Vargas takes the place of Alou, who hadn't played since May 12 with a pulled left quad. The Mets placed him on the disabled list retroactive to May 13, meaning he'll be eligible to play again on May 28. The left fielder had been batting .318 with two home runs in 110 at-bats.
In Alou's absence, normal backup Endy Chavez has been splitting time with 21-year-old rookie Carlos Gomez, who took Pelfrey's roster spot over the weekend.
The Mets suffered one other injury Wednesday night, when shortstop Jose Reyes left the game in the eighth inning with a cramped left hamstring. Neither Randolph nor Reyes viewed the injury as serious, and the shortstop expects to play Thursday.
Anthony DiComo is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.