Bernal was distanced by winner Primoz Roglic (Jumbo-Visma) inside the final kilometre but had looked strong on the testing finishing circuit around Bologna at the end of a tough 206 kilometres.
The reigning Tour de France champion forced a late selection with an attack on the penultimate ascent of the fearsome San Luca climb and will continue his preparations for the final Monument of the season in tomorrow’s GP Beghelli.
Diego Rosa also impressed in the Italian Classic, attacking on the first of five ascents of the 2km San Luca climb, before riding strongly on the final climb to bring a small group of late attackers back to Bernal’s group.
Tao Geoghegan Hart also did fine work in support of Bernal, while Ivan Sosa and Gianni Moscon hung in to the ever reducing front group until the closing stages.
The same Team INEOS lineup will tackle tomorrow's GP Beghelli, another punchy test on the road to Lombardia.