Molano beat out Mads Pedersen (Trek-Segafredo) and teammate Pascal Ackermann to the line for his first WorldTour stage win as UAE Team Emirates completely controlled the finale.
The bunch finished together behind them with the overall contenders times' unchanged, Evenepoel winning the race by 2 minutes and 2 seconds over Enric Mas (Movistar) and 4 minutes and 57 seconds ahead of Juan Ayuso (UAE Team Emirates).
Ayuso's third place at just 19-years-old makes him the youngest rider to tally a GC podium place in the WorldTour since 1931.
Pedersen sealed the points classification title after amassing a huge lead throughout the race, while Richard Carapaz (INEOS Grenadiers) was crowned King of the Mountains after moving from second to first when leader Jay Vine (Alpecin-Deceuninck) abandoned in Stage 18. Evenepoel took out the best young rider classification to go along with his overall victory.
The stage began as expected, with the peloton cruising into Madrid and all but the sprinters and a few breakaway hopefuls expected to contest the racing on the day.
Alejandro Valverde (Movistar) was able to enjoy his final Grand Tour stage in his home country with 50 kilometres to go, the Spaniard going on a solo lap out in front to take in the adoration and applause from the thousands of fans on the side of the road.
Attacks began at the 45 kilometre mark before a two-man break got away with Julius Johansen (Intermarché-Wanty-Gobert Matériaux) and Australian Luke Plapp (Ineos Grenadiers).
The pair held an advantage through the technical city circuit all the way into the final 3 kilometres before UAE Team Emirates and Alpecin-Deceuninck decided enough was enough, swallowing them up just inside the flamme rouge.
It was then the UAE and Molano show in the final kilometre, the Colombian too quick for the rest of the challengers as he beat the green jersey Pedersen to the line.
A jubilant Evenepoel punched the air as he finished in the red jersey to seal an emphatic Grand Tour victory, the 22-year-old battling through hardship and criticism to cement himself as one of the best young riders in world cycling.
