Carlos Corporan followed George Springer's two-out infield hit, which tipped off of Gonzalez' glove, with a two-run homer. Gonzalez then gave up a walk, a double and hit a batter to load the bases before escaping on a flyball out.
"That hit over the head stirred the pot," Gonzalez said.
Up until Springer's hit, the Nationals' left-hander looked dominant.
"I feel like I went out there and attacked the strike zone," he said after his second start. "(I am) right where I want to be. My arm felt great. Take away that one hit, I think the game would have been a little bit different."
Of perhaps more concern to the Nationals is that closer Rafael Soriano had his second rough outing, giving up five runs on five hits in just 2-3 of an inning.
In his previous outing, Soriano gave up two runs on three hits in an inning. His spring ERA is now 37.80.
"Right now, I'm concerned about how he feels, not necessarily the results," Nationals manager Matt Williams said. "He's going to get a few outings this spring and I want him to progress arm strength-wise every time."
From that standpoint, the outing was positive.
"When I asked him how he felt today, he said, 'That's the only good part of today,'" Williams said.
Houston starter Lucas Harrell allowed one run and recorded 10 groundball outs in four innings.
Astros: Harrell threw 49 pitches over four innings, then went to the bullpen and threw 10 more just to stretch his arm out just a little more.
The Astros right-hander gave up a run on two hits and recorded 10 of 12 outs on groundballs. Six of those grounders went to second baseman Gregorio Petit.
"He was everywhere," Harrell said of Petit. "Every time they hit the ball, I felt like it didn't matter if it was on the third base side, he was going to go get it.
Nationals: RHP Doug Fister (elbow inflammation) is expected to start a throwing program Tuesday. He will play catch on flat ground and then be evaluated before the team makes further plans. Fister felt discomfort in his elbow after making his first spring start on March 2.
"We've got to make sure he's good to go with every step," Williams said. "That's the first one."
Right-handers Ross Ohlendorf (back spasms) and Ryan Matheus (chest inflammation) are also throwing on flat ground and are working their way back toward game action.
Astros: center fielder Dexter Fowler was hit by a pitch in the second inning and was in noticeable pain on his way to first. Fowler said the ball hit him on his left foot.
"It should be fine," Fowler said. "It's a little sore, a little tight. Hopefully, it won't swell up too much."
The Astros made their second round of cuts this spring, optioning left-hander Luis Cruz, right David Martinez, outfielder Domingo Santana and catcher Matt Stassi to minor league camp. The team now has 52 players remaining in its big league camp.
Left-hander Michael Gonzalez, recently signed to a minor league contract, threw his first bullpen session on Sunday and will throw in a minor league game Tuesday before cycling into the Nationals relief rotation.