The strikes are the latest in a series of attacks and counterstrikes between Israel and Houthi militants in Yemen, part of a spillover from the war in the Gaza Strip.
The Israeli military said it had struck military camps, the headquarters of the Houthi military "propaganda" department, and a fuel storage site.
The Houthis' military spokesperson denied in a statement later that Israel had targeted missile launchers.
"Its strikes targeted purely civilian targets," he said.
He added that the offices of two newspapers had been targeted and that journalists and passers-by had been killed or wounded in those attacks.
He gave no figures.
Sanaa residents told Reuters the attack had targeted a hideout between two mountains that is used as a command and control headquarters.
The extent of any damage was not immediately clear.
The Israeli strikes also targeted the Houthi defence ministry, witnesses said.
The attack came days after an August 30 strike on Sanaa killed the prime minister of the Houthi-run government and several ministers, in the first such assault to target senior officials.
"The strikes were carried out in response to attacks led by the Houthi terror regime against the State of Israel, during which unmanned aerial vehicles and surface-to-surface missiles were launched toward Israeli territory," the Israeli military said.
The Houthi rebels have attacked vessels in the Red Sea in what they describe as acts of solidarity with Palestinians in the Gaza Strip.
They have also fired missiles towards Israel, most of which have been intercepted.
Israel has responded with strikes on Houthi-controlled areas of Yemen, including the vital Hodeidah port.
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