"It's a tough loss," Kennedy said about Thursday. "I feel like losing last night the way we did, and losing how we did today, it's always really tough when you lose these close games."
Kennedy (3-1) lost for the first time since Aug. 18, 2011, a span of 12 starts. The right-hander allowed two runs on four hits over seven innings.
The Nationals' Ross Detwiler, though, was better, as he held Arizona to just one run before leaving with one out in the seventh.
"Ian pitched a great game, but so did their guy, Detwiler," D-backs manager Kirk Gibson said. "We were just unable to get on him and get some runs across."
The first Washington run came in the second, when Rick Ankiel's groundout scored Jayson Werth.
Werth had advanced from second to third during Ankiel's at-bat when second-base umpire Jeff Nelson called a balk on Kennedy, saying he didn't come set before throwing the pitch.
"He said I didn't stop, but I didn't feel like I did anything different," Kennedy said referring to the earlier pitches in the at-bat. "That's what was really confusing. That's why I didn't know what he was talking about."
Without the balk, Werth would not have scored on the groundout, and the inning would have been over after the next batter, Wilson Ramos, popped out.
The D-backs managed to tie the game in the sixth when Willie Bloomquist drew a one-out walk and scored when Aaron Hill followed with a double to right-center that landed just out of the reach of a diving Werth.
"I think we played pretty good baseball," Gibson said. "Sometimes you come out ahead, and sometimes you don't. The guys played good, they played hard. Both teams pitched well, played well, they got more guys in than we did tonight. We feel good about ourselves, and we'll come back tomorrow."
The game did not stay tied for long in the sixth. As he did in Wednesday's game, rookie phenom Bryce Harper played a big role at a crucial time.
Ian Desmond led off the bottom half of the inning with a double to left, and he moved to third on a sacrifice bunt by Steve Lombardozzi.
That brought Harper to the plate, and Kennedy got him to foul off a 90-mph fastball to start the at-bat.
Catcher Miguel Montero then set up inside for a fastball, but the pitch ran back out over the middle of the plate, and Harper lined it a few feet inside the left-field line to give the Nats a 2-1 edge.
"It was just a bad pitch," Kennedy said.
"I knew I had to get something deep in the outfield, basically through the hole," Harper said. "Kennedy is a great pitcher. He has great offspeed stuff. That changeup is very good. I was trying to wait back on something, and I got something to drive."
Harper, who made his home debut in Tuesday's series-opening game, was a thorn in Arizona's side the past two days, going 4-for-7.
"He had a good series against us," Gibson said. "He's very impactful in their lineup, and played great for them. He had a huge impact in their two wins."