The Popular Movement (MP) and the National Rally of Independents (RNI) won 43 and 38 seats respectively, followed by the Socialist Union of Popular Forces (USFP) with 36.
The USFP is the dominant party in the ruling coalition, with Istiqlal as a junior partner.
The Constitutional Union party occupied the sixth position with 27 seats.
The provisional figures showed a record-low turnout of 37 per cent.
But Reda Lamrini, a political analyst in Rabat, told Al Jazeera that regardless of the turnout, the elections represented "year zero for democracy in Morocco".
"The 41 per cent is a reflection of the turnout. Lets keep this number today and compare it to the number we are reaching five years from now," he said.
The parties from the ruling coalition together won 102 seats.
A total of 34 women have also been elected.
A complex voting system made it almost impossible for any group to win an outright majority, and whatever the outcome, real power will remain with the king, who is executive head of state, military chief and religious leader.
PJD disappointed
The PJD had expected to fare much better and aimed to become the biggest party in parliament, but scaled back its ambitions after polling closed on Friday.
On Saturday its leaders accused unnamed opponents of buying votes to skew the results of a poll marked by a record-low turnout.

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"There are no chances of Islamic groups winning as most people in Morocco are enjoying its liberal culture"

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"Dirty money has been flowing into the voting system. We have the proof and we will challenge this," Lahcen Daoudi, PJD deputy leader, told supporters in Rabat.
"It is not only sad for us, it is sad for Moroccan democracy."
Hashem Ahelbarra, Al Jazeera's correspondent in Rabat, the kingdom's capital city, said Istiqlal - the election's big winner - was traditionally strong in rural areas but never very popular in the cities.
However, if it were invited to form the next coalition government, Istiqlal might need partners from among the very parties at whose expense it has made gains.
Average voter turnout in rural areas was 43 per cent and in urban areas, it was 34 per cent. At 27 per cent, the turnout was lowest in Casablanca, one of Morocco's main cities, officials said.
A total of 20 cases of violation of electoral rules were registered, they said.