In Moscow the authorities rejected an application from Navalny's supporters to protest in the city centre, raising the possibility that the police may disperse the rally by detaining people, as they have often done in the past.
Government plans to raise the state pension age to 60 for women and 65 for men, from the current 55 and 60, have also seen Putin's approval ratings take a major hit.
Navalny didn't take part in the protests, as he's now serving a 30-day sentence for violating public demonstration laws. A total of 452 people were detained there, while in Moscow, 43 people were held after authorities had denied an application to hold a rally, the group said.
More than 2,500 people gathered in Moscow's Pushkin Square shouting "Putin is a thief!" and "No increase in the pension age!" The ruling party also lost seats in some regional parliaments to members of the Communist Party and the Liberal Democratic Party of Russian Federation, the news agencies reported, citing election officials.
"The authorities are not listening to people and that means it's time to take to the streets", Navalny's team said in a pre-protest statement.
Video footage from the demonstration in the Siberian city of Novosibirsk showed a tense standoff between riot police and protesters, who chanted "shame, shame".
"I have come here to protest against the pension reform, I have to live in this country and I want to have hope for the future and a good old age", said 22-year-old Nikolai Borodin.
Ahead of the vote a Moscow court jailed Navalny for 30 days, just a couple weeks before he planned to stage a rally against a deeply controversial pension reform on election day.
It is known that two criminal cases over the use of violence against police officers are initiated.
Fourteen journalists were detained and another three beaten up, said the Trade Union of Journalists and Media Employees, an independent group. The president responded by offering some concessions, but argued that the age hike is necessary because rising life expectancy in Russian Federation could exhaust pension resources if the eligibility age remains the same.
The scale of the electoral setbacks for United Russia is "a unique situation", said Dmitry Orlov, a political analyst who's a member of the party's supreme council.