Thome and Pat Burrell each homered twice as Pujols went hitless in five at-bats to end his 30-game hitting streak in the Phillies' 9-4 victory over the Cardinals.
Pujols, who had missed the previous four games due to the flu and a two-game suspension, was a late addition to the Cardinals' lineup. He never came close to extending his streak - the longest in team history since Stan Musial's run in 1950 - grounding out in the first and fifth innings, striking out in the third and seventh and lining softly to short for the last out of the game.
One of the leading candidates for the National League Most Valuable Player Award, Pujols fell three games shy of the St. Louis record, set by Rogers Hornsby in 1922.
Thome made history for Philadelphia, belting two homers to raise his season total to 36, two more than Deron Johnson's record for most by a Phillies first baseman. It was Thome's fifth multi-homer game of the season and 31st of his career. Against Cardinals' pitching this year, he is 6-for-13 (.462) with five homers and nine RBI.
Burrell added two homers, including the 100th of his career in the seventh inning, for his fourth multi-homer game this year. It is the second time this season Thome and Burrell have hit multiple homers in the same game, also accomplishing the feat against Atlanta on April 9.
Rheal Cormier (4-0) was the beneficiary of Philadelphia's four-run eighth inning, gaining the win after tossing two scoreless innings.
Steve Kline (4-5) took the loss, yielding three runs and three hits while retiring just one batter on his 31st birthday.
Placido Polanco drove in two runs for the Phillies, who snapped a three-game skid and won for just the third time in their last 14 road games.
After Burrell's solo shot in the seventh drew Philadelphia within 4-3, the St. Louis bullpen imploded in the eighth. With one out, Kline relieved Jason Simontacchi and yielded an infield single to Bobby Abreu. The lefthander went to a 2-2 count on Thome and was upset when the fifth pitch was called a ball, running the count full.
Thome ripped that pitch for his second blast of the game, a two-run shot to right, to give the Phillies a 5-4 lead. Mike Lieberthal hit a shot to right that bounced over the wall for a ground-rule double, but Chase Utley fouled out. Esteban Yan came on to face Burrell, who deposited a 2-1 pitch over the left-center field fence for his 19th homer.
Yan continued to struggle in the ninth, as pinch hitter Ricky Ledee singled and took second on a wild pitch. Marlon Byrd drew a four-pitch walk and both runners advanced on a passed ball. Polanco and Abreu followed with RBI singles to make it 9-4 and Thome walked to load the bases, but Yan settled down and got Lieberthal to line out and Utley to hit into a double play to stop the bleeding.
Edgar Renteria put St. Louis ahead in the second with an RBI double, but Thome homered in the fourth to knot the game. Mike Matheny's run-scoring single gave the Cardinals a 2-1 lead, but Polanco plated Byrd with a groundout in the sixth to tie it.
The Cardinals got to Phillies starter Brett Myers for two runs in the sixth to build a 4-2 cushion. Tino Martinez drew a one-out walk and Renteria singled, but left fielder Burrell overran the ball, allowing both runners to advance. Matheny followed with a single to score Martinez and pinch hitter Orlando Palmeiro lifted a sacrifice fly.