Gnassingbe's Union for the Republic party (UNIR) won 108 of 113 seats in the new assembly, according provisional results announced by the national electoral commission.
Under the new constitution approved by lawmakers in April, Gnassingbe will now be able to take a new post as president of the council of ministers, a kind of prime minister role automatically assumed by the leader of the majority party in parliament.
Already in power for nearly 20 years, Gnassingbe succeeded his father Gnassingbe Eyadema, who ruled for almost four decades in the small coastal West African state between Benin and Ghana.
Opposition parties had denounced the reform as an "institutional coup" that created a role tailor-made for Gnassingbe to evade presidential term limits and extend his family's political dynasty. UNIR loyalists say the reform made Togo's democracy more representative.
Gnassingbe, 57, has already won four elections, though all were denounced as flawed by the opposition. The main opposition boycotted the last parliament election in 2018, citing irregularities.
According to the new constitution, Togo's president now becomes a mostly ceremonial role elected by parliament, and not the people, for a four-year term.
Togo's shift from a presidential to a parliamentary system means power now resides with the new president of the council of ministers, who will be the leader of the majority party in the new assembly.