Harris has never had a hit in 13 at-bats against Hernandez, and though the Mets were rallying, he was happy to see him leave.
Todd Coffey's first pitch, Harris punched a sharp single over first base to score two runs to lead New York to a 6-3 win over the Nationals on Sunday.
The pinch-hit single highlighted a four-run sixth inning, spoiling what was likely Hernandez's final game with Washington.
"I wasn't looking forward to facing him today, knowing those numbers," Harris said. "But, you know, it's the most comfortable 0 for 13 that I've ever had."
Hernandez, who started the Nationals home opener in 2005, made his final start of this season, and though he's indicated a willingness to return as a reliever, the team hasn't indicated that it would want him back.
Knowing that Hernandez's career here is probably over, the fans gave Hernandez (8-13) a warm ovation as he walked in from the bullpen to start the game, and a longer thank you when he left the game in the midst of the four-run inning.
"I've had a great career here," Hernandez said. "That was very nice. I appreciated the support."
Lucas Duda hit a long home run to center field with one out in the sixth to tie the score at 3.
After David Wright, Jose Pagan and Jason Bay singled to load the bases, Washington manager Davey Johnson walked out to hook Hernandez.
The 36-year-old pounded fists with his catcher, Wilson Ramos and infielders, shook Johnson's hand and trudged off the mound. Savoring his moment, Hernandez tipped his cap to home plate umpire Brian O'Nora and acknowledged the crowd's roars by waving his cap.
"I loved it," Johnson said. "I wish there was a better outing — a better ending."
The Mets won two of three against Washington, and after eight wins in their last 10 games, they're within two games of .500.
While the Mets won, it was Hernandez's day.
"I don't know what's going on — what's going to happen with me. I know what I want — and (we'll) see what's the answer," Hernandez said.
Ryota Igarashi (3-1) was the winner. After starter Mike Pelfrey walked the bases loaded with two outs in the fifth, Igarashi retired the only batter he faced.
Josh Stinson pitched two scoreless innings, Jason Isringhausen a scoreless eighth and Bobby Parnell the ninth for his fifth save.
The Mets scored two runs off Hernandez in the third. Josh Statin led off with a single — his first major league hit. Nickeas followed with a single. Pelfrey advanced them with a bunt and Ruben Tejada punched an opposite-field single to right to score both.