Jota, on loan from Atletico Madrid, opened the scoring with a left-footed strike in the 55th minute and Brazilian Bonatini completed the victory with an angled shot 16 minutes later.
Wolves are now two points clear of second-placed Cardiff City, who were beaten 1-0 by Birmingham City on Friday.
Sheffield United are third after Chris Basham’s close-range header gave them a 1-0 win over Ipswich Town at Bramall Lane on Saturday.
Preston North End moved up to fifth despite being held to a 2-2 draw by Fulham. First-half goals from Jordan Hugill and Sean Maguire had put Preston on course for victory but Oliver Norwood cut the deficit with 16 minutes left and Denis Odoi scored a 96th-minute equaliser.
Leeds United dropped to sixth after suffering a 1-0 defeat at home to Reading, with former Leeds loanee Modou Barrow scoring the winner.
Bottom side Bolton Wanderers claimed their first win of the season by beating Sheffield Wednesday 2-1 thanks to Sammy Ameobi’s opener and a Sam Hutchinson own goal. Bolton are now on five points, six points from safety.