Officers were called to The Islamic Centre in Newton Heath, Manchester, at about 01:20 BST.
Two men dressed in black were seen running from the scene, police said.
The fire was started just hours after two men ripped CCTV cameras from the Regent Street building's walls, at about 23:30 BST on Friday.
Police said the offenders were black men in black clothing with scarves covering their faces.
Insp Chris Hadfield, of Greater Manchester Police, said: "We believe the two incidents are linked and that the theft of the CCTV cameras was meant to help them carry out their arson attack on the minibus without being recorded.
"Fortunately there are several other cameras that capture the rear of The Islamic Centre, where the attack took place.
"We are investigating the possibility that this is a targeted hate crime."

The men, who are in their mid 20s, were caught in squally conditions after they left Raasay at about 20:00 on Sunday to paddle across about a mile of sea.
The mother of one of the men raised the alarm before later finding them on the shore of The Braes peninsula on Skye.
The Coastguard said the men were "very  cold" and needed medical attention.
The Portree RNLI lifeboat and Coastguard Rescue Team had been looking for the two men.
After the kayakers were found, the lifeboat crew took them to Portree Hospital where they were treated for hypothermia and cuts and scrapes.
The Coastguard team escorted the mother and another woman safely back home.
Coastguard watch manager Martin Collins said: "These kayakers have been very lucky.
"We have had wintery squalls across the area this evening with winds gusting to over 40mph at times and if they hadn't made someone aware of their plans they could have been exposed to the elements for a lot longer.
"If you are heading out to sea in a kayak the Coastguard recommends that you check the weather forecast and tidal conditions before you head out, wear a buoyancy aid and carry distress flares are in date and stowed where you can reach them."
He added: "For remote locations carrying a personal locator beacon is highly recommended."

Kuznetsova's 6-2 6-1 victory in Moscow ensured she took the eighth and final tournament spot.
Konta, who is in Singapore with the rest of the finalists, did not play this week due to an abdominal injury.
The Australian-born 25-year-old, ranked 10th in the world, will compete if any player withdraws.
Kuznetsova, 31, took just over an hour to defeat her 22-year-old Australian opponent on Saturday and qualify for her first WTA Finals since 2009.
"I was trying not to think about Singapore all week. I was playing match by match and I'm so happy to win," she said.
Kuznetsova will next face world number three Agnieszka Radwanska of Poland in Monday's group stages, before later games against Czech Karolina Pliskova and Garbine Muguruza of Spain.
Konta will finish her season at the WTA Elite Trophy for players ranked from ninth to 20th, which gets under way in Zuhai, China, on 1 November.
It will complete a season that has seen her named the most improved player of the year after she recorded seven victories over top-10 players, and became the first British woman to break into the top 10 since Jo Durie in 1984.
Arsonists set fire to a minibus belonging to a Muslim community centre in what police say may have been a "targeted hate crime".
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Two kayakers got into difficulty after their craft capsized in bad weather while making an evening crossing between the isles of Raasay and Skye.
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British number one Johanna Konta missed out on a place in the WTA Finals after Russia's Svetlana Kuznetsova beat Daria Gavrilova in the Kremlin Cup.