The 28-year-old left-hander had an MRI on Sunday that Nationals manager Matt Williams said showed ''no structural damage.''
''He's got some inflammation,'' Williams said. ''He'll be shut down for four to five days. No throwing, no nothing. Then we'll start him back on a program.''
Gonzalez (3-4) dropped his third straight start in Saturday's 5-2 loss to the New York Mets. He lasted only three innings, allowing five runs and seven hits, which raised his ERA to 4.62. Gonzalez gave up seven runs and nine hits in his previous start at Oakland.
General manager Mike Rizzo said before the MRI that Gonzalez would miss two starts after getting the MRI, in which dye is injected.
''The tests came back great,'' Williams said. ''We'll build him back up. Love to have him when he's ready.''
The Nationals recalled Ryan Mattheus from Triple-A Syracuse.
Gonzalez left a start in late April because of shoulder tightness.
''He passed a strength test. Combined having a little soreness (Saturday) with a little soreness a month ago, we thought this was a prudent way to do it,'' Rizzo said before Sunday's series finale with the New York Mets.
Gonzalez side-stepped questions about his health Saturday, but spoke with Rizzo following his latest loss.
''I don't have a great concern level for it right now just because the way Gio said he felt after the game,'' Rizzo said.
Gonzalez lost command of the strike zone Saturday, falling behind in the count and throwing 84 pitches in three innings.
''I thought he looked fine,'' said Rizzo about whether he saw an injured pitcher on the mound. ''His arm speed was good. His spin was fine. As good as it's always been on his breaking ball. His fastball velocity was good. The command part of it, which sometimes comes and goes with Gio anyway, was the thing that was causing him an issue.''
Gonzalez went 32-16 during his first two seasons with the Nationals after a trade with the Oakland A's. He made at least 32 starts in each of his previous four seasons.
''He's a big key to the ball club,'' Rizzo said. ''We'd like to get him back. We're going to take our time with him and be careful with him because he's vital to the ball club.''
Mattheus has 140 career appearances with the Nationals, including two this season. He has not allowed a run in three innings.