For the 10th year in succession at the Circuit de Catalunya, the driver who started on pole position took the chequered flag as winner.
"It was a fantastic result and I'm absolutely thrilled," he said after his third career win.
Spaniard Alonso, celebrating his first home race for the Italian team, inherited a crowd-pleasing runner-up position when McLaren's [ Images ] hard-charging Lewis Hamilton [ Images ] crashed out with a suspected suspension failure on the penultimate lap.
Red Bull's Sebastian Vettel [ Images ], who had started on the front row alongside Webber, finished third despite suffering brake problems.
Seven-times world champion Michael Schumacher [ Images ] was fourth, the best result so far of the 41-year-old's comeback season, with McLaren's Jenson Button [ Images ] unable to find a way past and forced to settle for fifth.
Button, Hamilton's team-mate and reigning world champion, stayed top of the standings with 70 points to Alonso's 67 after five of the season's 19 races.
Ferrari's Brazilian Felipe Massa [ Images ] was sixth, Germany's [ Images ] Adrian Sutil [ Images ] seventh for Force India [ Images ] and Poland's Robert Kubica [ Images ] eighth for Renault [ Images ].
Williams returned to the points with Brazilian Rubens Barrichello [ Images ] in ninth place and local youngster Jaime Alguersuari took the final point for Toro Rosso at his home track.
The biggest challenge Webber faced, after holding off Vettel's attempts to squeeze past at the start, was keeping alert as he lapped in splendid isolation and headed for a seemingly inevitable triumph.
Webber was the fourth different winner in five races.