San Diego receives minor leaguer Jean Cosme in the deal.
The museum at the AleSmith brewery in Miramar is expected to open in time for the 2016 All Star Game.
The 39-year-old played for Seattle and the Chicago Cubs last season.
"We are thrilled to partner with the Gwynn family."
The 34-year-old had played his entire 8-year career with the Chicago White Sox.
They're the first MLB games in Mexico City in 12 years.