Witnesses said the Djibouti army put down the revolt after a nearly 45 minute shoot-out with the police.
A state prosecutor said 12 policemen - including eight senior officers - were also indicted.
He said their trial is expected to take several months.
Last Thursday armed policemen surrounded the presidency after President Ismael Omar Guelleh sacked Mr Yabeh as the chief of staff of the National Police Force.
Witnesses said the Djibouti army put down the revolt after a nearly 45 minute shoot-out with the police.
The government said that two people died and six others were wounded in the fighting.
A French military officer speaking from Paris said the policemen had abandoned their positions after a few shots were fired.
"It looks like it was a fit of pique by the police because their boss was sacked. It's also possible that clan rivalries were involved," the officer told Reuters.
French troops based in Djibouti were confined to their bases during the trouble, he said.
Good friends
Many people assumed that the president and his police chief were good friends because they grew up together.
But tension between the two is reported to have been growing.
One report said President Guelleh had accused the police chief of not being in control of security in the capital.
Colonel Ali Hasan Omar was named as the new interim head of the police.