Milwaukee pitching had a three-hit shutout through 8 2/3 innings but Frazier, who hadn't hit a home run in more than a month, crushed a pitch from John Axford to right for his 19th home run of the year to tie the score at 1-1.
That saddled Axford with a Major League-high ninth blown save.
Jay Bruce followed with a single before Navarro finished off a nine-pitch at bat with a shot to the right-center that dropped in, allowing Bruce to score.
That handed Axford (5-8) the loss after he struck out the first two batters he faced.
Brewers pitching was in control until the Frazier home run. Milwaukee starter Wily Peralta allowed two hits over 5 1/3 innings but left the game with an undisclosed injury. He struck out six and walked one.
Brandon Kintzler gave up one hit in 2/3 innings while Francisco Rodriguez and Jim Henderson each chipped in one inning of no-hit, two-strikeout relief.
Cincinnati reliever Jonathan Braxton (4-3) got the win with an inning of two-hit pitching.
Milwaukee managed just five hits, including a third-inning home run by Carlos Gomez.