The maneuver ensures that Gomez – who signed with the Mets as a 19-year-old non-drafted free agent in 2002 – will be protected from the Rule V Draft.
That selection process will take place during the Major League Baseball Winter Meetings in Orlando, Fla. in early December.
Gomez shared an organizational Sterling Award – indicative of selection as his club's most valuable player – with first baseman Michel Abreu at Double-A Binghamton this season, jumping past Class-A St. Lucie after playing 2005 at Class-A Hagerstown.
Gomez finished the season batting .281 with seven home runs and 48 RBI, tying for second in the Eastern League with 41 stolen bases and tying for fourth with eight triples.
The performance left Gomez satisfied; near the close of the season, Gomez said his numbers could earn him a chance to play in the major leagues toward the tail end of 2007.
"I'm focused on playing the game and seeing what happens later," Gomez said in September. "I'll be ready for next year when we come for the big league camp. The manager (Willie Randolph) wants to see that you're ready.
"I want to be like that, play in (New Orleans) a couple of games and go to the big leagues. I'm ready. I can hit and I can steal. And defense? Don't worry about it."
Gomez projects to be one of the Mets' top prospects in 2007, along with pitchers Mike Pelfrey and Philip Humber, plus outfielder Fernando Martinez.