Barack Obama said the protesters had “legitimate grievances” but described the shooters as “criminals” who should be arrested.
The shootings on March 11 happened during a demonstration after it was announced Ferguson Police Chief Thomas Jackson would resign.
Further protests on March 12 passed peacefully. The two officers have been released from hospital.
The protests are the latest of many in the city since a policeman shot dead Michael Brown, an unarmed black teenager, in August 2014.
Police Chief Thomas Jackson quit one week after a Justice Department report alleged widespread racial bias in his department and the city’s court system.
Protesters gathered outside the police station after Thomas Jackson’s resignation was announced.
Late on Wednesday, one officer was shot in the face and the other was hit in the shoulder as protestors were heading home for the night.
“I think that what had been happening in Ferguson was oppressive and objectionable and was worthy of protest. But there was no excuse for criminal acts,” President Barack Obama said on the Jimmy Kimmel Live on ABC.
“Whoever fired those shots shouldn’t detract from the issue; they’re criminals,” he added.
Tensions have been high in Ferguson since August and escalated in November after a grand jury declined to prosecute Officer Darren Wilson for Michael Brown’s killing.
On March 12, protesters held a candlelight vigil for all victims of violence. They later marched to the police department while beating drums and chanting.
There were no rows of police officers in riot gear unlike previous demonstrations.
Ferguson police temporarily ceded security responsibilities for the protests to state troopers and county police.
The protests ended without a single arrest about 23:00 local time.
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