The National Rally for Democracy (RND) of Prime Minister Ahmed Ouyahia, a nationalist party close to the military and loyal to Bouteflika, was second with 68 seats, compared to 62 in the outgoing house.
While the results largely maintain the status quo, one notable change was the number of elected women, which rose to 145 from seven in the outgoing assembly following the introduction of quotas.
Algeria's governing coalition so far included the FLN, the RND and the largest of the legal Islamist parties, the Movement of Society for Peace.
Friday's provisional results, which have yet to be confirmed by the constitutional council, mean the FLN and the RND could form a majority without the Islamists.
Green Algeria, a three-party Islamist alliance, garnered a paltry 48 seats and charged widespread fraud.
"There has been large-scale manipulation of the real results announced in the regions, an irrational exaggeration of these results to favour the administration parties," it said in a statement.
The Movement of Society for Peace (MSP) -- the main party in the alliance -- marvelled that it did not obtain a single seat in the constituency of Blida, an Islamist bastion where the party was created.
"It exposes the people to dangers for which we do not want to take responsibility... We will take the necessary measures and will put the blame squarely on the the president of the republic," Green Algeria said.
In the wake of the popular revolts that became known as the Arab Spring, moderate Islamist parties recorded electoral victories in Tunisia, Egypt and Morocco.
Turnout had been expected to be low after a campaign that produced no new faces and failed to draw crowds.
But Interior Minister Daho Ould Kablia announced a "remarkable" rate of 42.36 percent which he said confirmed Algeria's democratic credentials.
Pro-government newspapers said voters had expressed confidence in the political system by taking part in the election, which comes after a reform package initiated in the wake of the Arab Spring.
"If there's a winner on this Algerian spring day, it's undoubtedly the people," El Moudjahid wrote in a front-page editorial.
The governing coalition and many Algerians argue that the country has already experienced the consequences of Islamism during the deadly 1991-2002 civil war and that the dynamics of the Arab Spring cannot apply in Algeria.
Ouyahia also argued that the Arab Spring was hardly an attractive scenario, calling it a "plague" that had resulted in "the colonisation of Iraq, the destruction of Libya, the partition of Sudan and the weakening of Egypt."
Many Algerians and observers had predicted that ever deeper mistrust, especially among the country's majority of young people, could lead to an even worse turnout than the historical low of 35 percent recorded in 2007.
The opposition Rally for Culture and Democracy, which chose to boycott this election, claimed the announced turnout was fraudulent.
"The turnout as recorded by the local commissions, infiltrated by the administration though they may be, did not exceed 18 percent," the party's chairman said at a press conference.
Some 500 foreign observers brought in by Bouteflika to monitor the vote reported only minor hiccups but they were denied access to the national electoral roll, which grew by four million voters since 2007.
Former colonial power France said it was pleased polling operations were smooth.
Bouteflika was a minister in Algeria's first independent government in 1962 and, at 75, he is keen to burnish his legacy with large-scale projects such as the world's third largest mosque.
Analysts say the legislative election was acting as a kind of primary for the 2014 presidential poll, which Bouteflika is not expected to contest.