Al-Assad, 41, was the only person allowed to put his name forward in the run-up to Sunday's plebiscite, which was boycotted by the opposition and widely regarded as a formality.
Bassam Abdel Majeed, the information minister, declared the results at a news conference.
"This great consensus shows the political maturity of Syria and the brilliance of our democracy and multi-party system," he said.
US criticism
In Washington, the US state department dismissed the vote, saying Syrians had not been given a choice.
"It's pretty hard to suggest that any kind of election can be free, fair or credible when you've only got one candidate, and that candidate receives about 98 per cent of the vote," spokesman Tom Casey said.
"I'm sure President Assad is basking in the glow of his ability to have defeated exactly zero other candidates and continue his misrule of Syria," he added.
Parliament, which is dominated by the ruling Baath party, held a session late on Tuesday to ratify the results.
"I declare Bashar al-Assad president for a second seven-year term starting on July 17. Only Bashar deserved a 'yes' for leading Syria to victory," Mahmoud al-Abrash, the speaker, told the chamber.