Flores, who played parts of five seasons with the Nationals from 2007-2012, finished 2-for-3 with two runs scored. Former Major League infielder Ronny Cedeno also picked up two hits for the Aguilas.
Criollos scored once in the second inning and third baseman David Vidal hit a two-run home run in the eighth inning to cut Venezuela's lead to 4-3. Shortstop Ivan De Jesus Jr. also had two hits and one RBI for Puerto Rico.
The Criollos will play Cuba on Friday afternoon. Venezuela will play Mexico's Aguilas de Mexicali on Friday night.
Vidal, who signed a Minor League deal with the Marlins in October, hit his second home run in as many games and continues to show his power. He hit .320 with 62 RBIs in 85 games for the Somerset Patriots in the Atlantic League last season.
PLAY OF THE GAME:
Flores' home run gave Venezuela a 3-0 lead in the second inning and was the early highlight of the afternoon. Two innings later, he scored what proved to be the game-winning run on a single by Cedeno and a throwing error by De Jesus to give Venezuela a 4-1 lead.
Jesse Sanchez, who has been writing for MLB.com since 2001, is a national reporter based in Phoenix. Follow him on Twitter @JesseSanchezMLB and Facebook. This story was not subject to the approval of Major League Baseball or its clubs.