Lindh's husband, Bo Holmberg, and their children, Filip, 9, and David, 13, were among those at the solemn service at the Ersta church, the BBC reported.
The hour-long ceremony was led by pastor Thorbjoern Larsson, a family friend.
Singer Tommy Koerberg performed Paul Simon's "Bridge over Troubled Waters" and actress Stina Ekblad gave the bible reading, the newspaper Aftonbladet reported.
Lindh was later buried at an undisclosed location.
A day earlier, world leaders and hundreds of mourners attended a public memorial service in front of Stockholm's city hall.
Also Friday, a judge ruled the 35-year-old Swedish man who is the key suspect in Lindh's slaying nine days ago, could be held for another week.
Lindh was respected worldwide and a leading candidate to be the next prime minister.