The three-time Olympian kicked clear in the final stages of the mass public run to win in 43:01, 17 seconds ahead of Australians Collis Birmingham and Martin Dent.
Kenya's Beijing Olympic marathon champion Wanjiru was fourth in 44:20 and 2004 Athens Olympic marathon gold medallist Baldini finished 11th in 45:42.
Wanjiru, 23, only arrived in Australia late Friday because of the hospitalisation of his daughter and said his tiredness had affected his form.
The man tipped to break Haile Gebrselassie's world marathon record next year, he wasn't at his best as he chose to sit in the leading pack rather than aggressively set the tempo out in front.
"Today (yesterday) was not my day," Wanjiru said. "I can come here to try again (next year), maybe to break the course record or world record for 15km."
Weidlinger and Birmingham ran away from Wanjiru at the 6.5km mark and the Austrian found something extra to shake off Birmingham just before the 10km mark and didn't look back in the final 5km.
"It's probably one of my biggest victories because I have beaten two Olympic champions with Baldini and Wanjiru and I have beaten the European champion Jose Manuel Martinez (who finished eighth in 44:58)," Weidlinger, 31, said.
"He (Wanjiru) showed from the start that somebody should lead with him and after 1.5km, I thought I feel good and I am in the race and in the rhythm so I tried to push a bit and split up the lead group.
"I realised that Wanjiru was not in his best shape so I tried to push the last 200 metres uphill and we lost him."
Australian Nikki Chapple won the women's race in 50:18 ahead of compatriot Benita Willis and British dual Olympian Helen Clitheroe. -- AFP
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