Benintendi trailed Segura at each update Major League Baseball released of the voting.
Benintendi remains eligible for the team, as an injury replacement.
Segura entered Wednesday's slate with a slash line of.329/.356/.467 (130 OPS+) with 24 doubles and 14 stolen bases.
This will be Segura's second All-Star appearance.
For the eight players not selected in the Final Vote, the All-Star dream is not officially over.
San Francisco Giants first baseman Brandon Belt finished second in the NL balloting, followed by Max Muncy of the Los Angeles Dodgers, Trea Turner of the Washington Nationals and Matt Carpenter of the St. Louis Cardinals.
The 28-year-old veteran entered Wednesday with 23 home runs, which is tied with Colorado Rockies third baseman Nolan Arenado for the NL lead, 64 RBIs, which is third in the league behind Eugenio Suarez and Javier Báez.
The Mariners made a big push to get Segura a ticket to Nationals Park for next week's All-Star activities after he was named one of five AL candidates for the Final Vote on Sunday. It's also well deserved after Segura's superb first half helped to anchor the Mariners infield and offense. The 89 Midsummer Classic will be televised nationally by FOX Sports; in Canada by Rogers Sportsnet and RDS; and worldwide by partners in more than 180 countries.