The stage was marked by overnight leader Geraint Thomas of Sky suffering an untimely mechanical problem and having to change bikes on the final climb, he lost 40 seconds on the day while his muted team leader Chris Froome was 1:10 off the pace on Saturday too.
Landa took 6:22:13 to complete the challenging stage by outsprinting Rafal Majka and George Bennett to the line.
The fourth stage on Saturday is a rolling 219-kilometer (136-mile) route from Foligno to Sarnano-Sassotetto, ending in a mountain-top finish.
Landa rode a quiet race but broke free of the peloton with 2.6 kilometers remaining and caught up with Majka, Ben Hermans and Fabio Aru, who attacked earlier in the 14-kilometer climb to the finish, at the foot of the local ski slopes.
"I just went all out and it was enough".
"I'm in a new team".
Thomas and team-mate Chris Froome, who started the day in third place, lost over 40 seconds to stage victor Mikel Landa, while BMC Racing's Damiano Caruso took over the blue jersey. The Italian rider has an 11-second lead over Wilco Kelderman with Landa a further 9 seconds behind.
World champion Tom Dumoulin is in ninth place at 33sec.
The fifth stage on Sunday will pay a tribute to Michele Scarponi as it ends in his hometown of Filottrano after a hilly, 178-kilometer route from Castelraimondo.
The race also suffered the loss of Giro d'Italia victor and world champion Tom Dumoulin, who fell and pulled out early and was later reported to have suffered only cuts and bruises.
The race ends on Tuesday with an individual time trial in San Benedetto del Tronto.
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