Navalny, a Kremlin critic and anti-corruption campaigner, was laid to rest at a cemetery not far from where he once lived in the Russian capital, the Reuters news agency reported.
He died at the age of 47 in an Arctic penal colony on February 16, prompting accusations from his supporters that he had been murdered.
The Kremlin has denied any state involvement in his death, according to Reuters.
Thousands of mourners on Friday gathered to bid a final farewell to Navalny at the cemetery and earlier outside the Soothe My Sorrows church in southeastern Moscow where the funeral service took place, Reuters reported.
It said many people brought flowers and some chanted "Russia will be free," "No to war," "Russia without Putin," "We won't forgive," and "Putin is a murderer."
Kremlin spokesman Dmitry Peskov said he had nothing to say to Navalny's family.
Navalny's widow, Yulia Navalnaya, warned this week that Russian President Vladimir Putin, of whom her husband was a fierce opponent, "is capable of anything" and cannot be negotiated with.
Addressing the European Parliament on Wednesday, Navalnaya accused Russian authorities, led by Putin, of having orchestrated her husband’s killing.
'Putin must answer for what he has done to my country'
She also told European lawmakers that "tens of millions of Russians" were "against Putin, against the war, against the evil he brings."
She stated: “Putin must answer for what he has done to my country. Putin must answer for what he has done to a neighbouring peaceful country. And Putin must answer for everything he has done to Alexei.”
Navalnaya said last week that she would continue her husband's fight for "a free Russia."
"I want to live in a free Russia, I want to build a free Russia," Navalnaya said in a video message released three days after her husband's death.
Western leaders, including Poland's president, prime minister and top diplomat, have paid tribute to Navalny for standing up to authoritarian rule.
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Source: Reuters, IAR, PAP