WASHINGTON -- The clutch bat of Bryce Harper helped overcame a multitude of mistakes by his teammates Sunday afternoon.

Left fielder Jayson Werth made an error that led to a run in the eighth, catcher Matt Wieters dropped a throw that led to a run in the ninth and the Washington Nationals bullpen continued to fold in the late innings.

But the dramatic Harper, batting with a full count and two outs in the last of the ninth, cranked a three-run homer over the fence in center off 39-year-old closer Joaquin Benoit as the Nationals beat the Philadelphia Phillies 6-4, taking two of three games in the series.

It was the second homer of the game for Harper, who had five RBIs and lifted his average to .333.

"Two good swings right there," said Harper, who fell behind 0-2 in the count in the ninth. "Somehow I got it to 3-2. I did the best I could."

Has Harper, who had three hits, put a rough 2016 season behind him?

"I am just trying to stay healthy and play as many games as I can. It is fun," he said of his fourth career walk-off homer and first in nearly two years.

The Phillies, who have had their own issues with closers, were one pitch away from taking two of three from Washington for the second weekend in a row. Benoit got the save Saturday after Jeanmar Gomez began the season as the team's closer.

"Walks seem to score when we issue them," said Phillies manager Pete Mackanin, referring to the one-out walk to Chris Heisey to start the rally in the ninth.

Mackanin visited the mound before Harper went deep.

"I wanted to know how Benoit was going to pitch to him," said Mackanin, aware that Daniel Murphy (.396) was on deck after Harper. "Harper and Murphy back-to-back are tough. We just couldn't hold the lead in the ninth inning."

The loss was the fifth in six games and spoiled another strong performance by second baseman Cesar Hernandez, who had three hits from the leadoff spot and is hitting .346.

"Obviously, Harper was gearing up for a fastball," Mackanin said of the game-winning blast. (Benoit) "challenged him."

The Phillies have just two saves this year.

The winning pitcher was Shawn Kelley (2-0), who got the last out in the top of the ninth with the bases loaded, while Benoit fell to 0-1.

Aaron Altherr doubled to lead off the ninth and scored on a fielder's choice to break a tie and give the Phillies a 4-3 lead.

Altherr was on third after a groundout and then scored when Freddy Galvis hit a grounder off reliever Blake Treinen to second baseman Murphy. His throw was in time to catcher Wieters, who dropped the ball as Altherr scored. The Phillies left the bases loaded as Kelley retired Maikel Franco to end the ninth.

Washington starter Gio Gonzalez, who gave up three runs (two earned) in 7 1/3 innings, retired 10 batters in a row before Hernandez singled with one out in the eighth. Gonzalez then allowed a single to Daniel Nava and Hernandez scored as the ball got past left fielder Werth for an error. Koda Glover then gave up an RBI single to Tommy Joseph as the Phillies tied the game at 3.

"The bullpen has been struggling a little bit," said Washington manager Dusty Baker, understating the obvious. "We have to get better at fundamental plays. Extra outs always cost you."

Harper broke a tie with a two-run homer in the third as Washington took a 3-1 lead. His third homer of the year also scored Anthony Rendon (two hits), who reached on an infield single that was upheld after a Phillies replay challenge with two outs.

The Nationals had tied the game at 1 in the last of the first on an RBI double by Rendon.

Hernandez of the Phillies led off the game with a solo homer to left on a 90 miles-per-hour fastball on a 2-0 pitch from Gonzalez. It was the second homer in as many at-bats for Hernandez, who hit a homer in the eighth inning Saturday and then led off a game with a homer for the second time this season Sunday.

Jerad Eickhoff, the Phillies starter, gave up eight hits and three runs in six innings in his shortest outing of the year. Eaton had three hits for Washington.

"We were very fortunate to win this game," Baker said.

NOTES: Phillies manager Pete Mackanin was drafted in the fourth round by the American League Washington Senators (now Texas Rangers) in 1969. ... Nationals RHP Max Scherzer (1-1, 2.13) will face Atlanta RHP Mike Foltynewicz (0-1, 6.35) on Tuesday in new Sun Trust Park. ... The Phillies are also off Monday and will face Mets RHP Zack Wheeler (1-1, 7.45) on Tuesday in New York. ... The Phillies made just their third error of the season when 3B Maikel Franco threw the ball past first on an infield single by CF Adam Eaton in the fifth.