Russian Shubenkov came from behind to catch McLeod before the last hurdle but was tripped just ahead of the finish by the stumbling Jamaican while still somehow managing to fall forward over the line first to claim victory in 13.12 seconds.
McLeod's tumble meant he ended up fifth as the 28-year-old Shubenkov won an early morale booster ahead of one of the most anticipated clashes at the World Championships in Doha in September.
Sprinter Andre de Grasse seemed to have put last year's injuries and illness woes behind him with a strong late burst that left Turkish world champion Ramil Guliyev trailing in the 200m in another indicator of potential drama to come in Qatar.
Yet it was not a result that entirely satisfied the Canadian, who won in 20.19 sec.
"I was grateful for the victory but not happy with the time. I wanted a sub-20 seconds. But it's a long process," said De Grasse.
"I'm not yet fully healthy and still have a lot of work to do to be really back in shape. But I have time before the World Championship."
With Caster Semenya not participating following a war of words over her late invitation to compete in the Moroccan meet [nL8N23M0L1], the women's 800 metres was won by Kenyan Nelly Jepkosgei, in one minute 59.50 seconds.
But the best women's performance came in the 1500 metres where world record holder Genzebe Dibaba, of Ethiopia, ran the fastest time of the year to hold off her Dutch rival Sifan Hassan and win in 3:55.47.
The 30-year-old Nigerian, Blessing Okagbare, was a surprise victor in the women's 100m in 11.05sec, finishing ahead of Ivorian Marie-Josee Ta Lou with Dafne Schippers, a medallist at the last two world championships, only finishing fifth.
Salwa Eid Naser, of Bahrain, held off Niger's exciting youngster Aminatou Seyni to win the women's 400m for her third Diamond League triumph this year, in a season's best 50.13.
(Reporting by Mark Gleeson in Cape Town; editing by Ian Chadband)
