It was the Venezuelan's maiden F1 win and the first for any driver from his native country.
The margin of victory for his FW34 race car over Alonso's F2012 was 3.1 seconds in the race in Barcelona.
Kimi Raikkonen brought the Lotus Renault E20 home third, 3.8 seconds back.
"It's a wonderful day, not just for me but for all the team. We have been pushing so hard since last year to try to improve race by race and here we are," Maldonado said. "The car was so competitive since the first lap. Fernando did a better start than me but I was just following the pace and it was so great. It's my first podium and my first victory and you can imagine what I feel!"
Alonso led from the start, making a better jump off the line than Maldonado and led by as many as three seconds through the first stint. This duo left the balance of the field in their wake as they performed a paso doble on the balance of the F1 teams and drivers.
Behind the podium, Romain Grosjean took fourth for Lotus Renault followed by Kamui Kobayashi in the Sauber, Sebastien Vettel for Red Bull Racing, Nico Rosberg in the Mercedes, Lewis Hamilton for McLaren, teammate Jenson Button and Nico Hulkenberg taking the final point, one lap down for Sahara Force India Mercedes.
Kamui Kobayashi - Sauber F1 Team photoEnlarge Photo
There were the usual skirmishes in the first turn, with Sergio Perez' Sauber ending up having to pit for new rubber at the end of a first, slow lap. After the first round of pit stops for the leaders, Williams' Bruno Senna got together with Romain Grosjean (Lotus) on the 12th lap with light, bodywork-only contact.
That wouldn't be it for the Brazilian as he was punted by seven-time champion Michael Schumacher, ending the German's day immediately and Senna's later in the lap. Schumacher received a five-position Monaco penalty for his actions.
McLaren's pit woes continued as Hamilton ran over an object (likely a tire) as he exited his first pit stop, rejoining the field on the 16th lap in 14th position, up from 24th. By this time Grosjean passed Nico Rosberg to set off after Raikkonen and the two leaders but seemingly unable to break into their train.
Maldonado's in-lap before his second, lap 25 pit stop was a scorcher as he attempted to get ahead of Alonso--and he did so. During this period reigning champion Sebastian Vettel received a drive-through for failing to slow for a caution flag, as did Felipe Massa in the second Ferrari.
That would allow Hamilton to leapfrog the Brazilian, who had been making life difficult for the 2008 titleholder. Hamilton made his second and final stop on the 36th lap for hard Pirelli tires--it was a clean stop this time around--and he rejoined behind Paul di Resta's Sahara Force India Mercedes in 14th.
Grosjean leads a train - Lotus F1 Team photoEnlarge Photo
The Venezuelan took the lead for good on the 47th lap with an enviable move into the first turn; Alonso did the same on the 49th lap using the DRS zone to retake P2. And so they would battle to the close, with the younger, less experienced Maldonado showing the cool of a true veteran.
Alonso "took the momentum" from his great start "and we led the race for the first part, but then Williams' anticipated the stop and get in front and at the end it was close. In the very last laps," Alsonso explained, "I felt the car was strange; we lost a lot of grip. We were lucky at the end; second place at home feels fantastic--hopefully this is a step forward in terms of championship possibilities."
Despite gaining another podium, Raikkonen was disappointed not to take the victory. "If everything had gone right in the first part of the race we could have won," he said. "Our car can do it, but everything has to fall into the right place to be able to get on to the top step. So far we've made good steps forwards; the car feels strong everywhere."
With this victory, Maldonado became the fifth winner in as many races, and the team celebrated founder Sir Frank Williams' 70th birthday this weekend. But it wasn't all joy in the Williams camp as a fire broke out after the race that decimated the car of poor Senna and injured 16 paddock members that came to the aid of the Williams team with their fire extinguishers, one seriously. The fire spread to neighboring pit boxes; reserve driver Valtteri Bottas said he "felt an explosion from behind, somewhere in the fuel area and everyone ran out quickly." There were no reports of injury to team owner Williams.
There's now a tie between Vettel and Alonso for the lead in the drivers' championship, with Hamilton, Raikkonen and Mark Webber filling out the top five. Red Bull Racing leads the constructors title with McLaren 11 points back, Lotus third, Ferrari fourth and Williams tied for fifth with Mercedes.
The next race takes place at Monaco the final weekend of the month. Will we have a sixth new winner there?