Upton had hoped to participate in the event, which will be held the day before next Tuesday's All-Star Game at Chase Field.
"I would have loved to have been picked to have been in it, just for the sole fact that it's in my stadium and hopefully a lot of our fans are there," said Upton. "That would have been awesome, but at the same time [now] I get to sit back and enjoy it."
Instead, Fielder, as captain of the team, chose teammate Rickie Weeks, Cardinals outfielder Matt Holliday and Dodgers outfielder Matt Kemp.
"It was very tough, I wanted everybody to be in it," Fielder said. "I definitely wanted someone from the Diamondbacks to be in it, but these guys, I know these guys really well, and these are my picks, no hard feelings."
Fielder was asked before the game if he talked to Upton about it.
"I don't know, man, it was just tough," Fielder said.
Upton hit a home run Tuesday night against Fielder's Brewers and said he chatted with the first baseman when he reached on a single in the first.
"I said what's up, as usual," Upton said. "There's no hard feelings at all."
American League captain David Ortiz selected Red Sox first baseman Adrian Gonzalez, Blue Jays outfielder Jose Bautista and Yankees second baseman Robinson Cano.