Pena drove in a run in the first inning and homered in the fourth to give the Astros a 2-1 lead they never relinquished.
The Phillies, who were no-hit in Game 4, had six hits Thursday, but scored only two runs.
They strewed the basepaths with stranded runners Thursday, leaving 12 on base and going 1 for 7 with runners in scoring position.
Late in the season the Phillies were not expected to win their way into the playoffs, let alone be in position to win only their third World Series in the team’s 139-year history.
But they are in dire straits.
This is a team more associated with losing than winning. The Phillies have finished last 34 times. From 1933 to 1945 they finished last or next to last 13 straight times.
After four Astros pitcher threw a no-hitter at them in Game 4, Phillies manager Rob Thomson told his team, “Hey, the last time we got no-hit, we ended up coming back and winning the next day.”
That, too, was a combined no-hitter by the Mets in New York in April and the Phillies won the next day, 4-1.
But this time it was not to be.
Verlander was in trouble numerous times, but worked his way out of it, mostly because most potential Phillies rallies began with two outs.
Houston gave Verlander a quick lead in the top of the first when Jose Altuve doubled and took third when center fielder Brandon Moss bobbled the ball for an error.
Pena singled to center and Verlander had a 1-0 lead. Further damage was avoided when Jose Alvarez struck out and catcher J.T. Realmuto threw Pena out at second base.
The lead lasted only until his second pitch in the bottom of the first.
Middletown native Kyle Schwarber launched one into the right field seats, his third World Series leadoff home run, tying the record with his 51st home run this season.
Philadelphia’s first two were retired in the second, but Jean Segura singled and Verlander walked Marsh and Schwarber to fill the bases.
Verlander escaped by striking out Rhys Hoskins.
Verlander walked Bryce Harper with one out in the third. Nick Castellanos blasted a bullet, but shortstop Pena made a leaping catch.
Alec Bohm singled to left, putting runners on second and first with two outs. Verlander enacted another escape act by retiring Bryson Stott on a fly to right.
Pena gave Verlander a 2-1 lead in the fourth with a leadoff home run off Phillies starter Noah Syndergaard, the first rookie shortstop in post-season history to hit a home run. And it knocked Syndergaard out of the game.
Verlander pitched a 1-2-3 fourth. He struck out the first two in the fifth, then was hit for a double by Harper, putting the potential tying run on second.
Castellanos put together a 10-pitch at bat before flying to shallow left, Verlander’s last batter.
The Astros added their third run in the eighth against Seranthony Dominquez on a walk to Altuve, Pena’s single for his third hit, and a ground ball RBI by Alvarez.
The Phillies put together a rally in the eighth that finally produced something, and they did it against one of Houston’s best bullpenners, Rafael Montero.
Montero walked Castellanos to open the inning. After Bohm struck out, Montero walked Stott. Jean Segura singled for a run, ending the Phillie futility streak of 0 for 19 with runners in scoring position.
Astros manager Dusty Baker pulled Montero and inserted closer Ryan Pressly. He struck out Marsh on three pitches and Schwarber was retired on a crushed ground ball to first baseman Trey Mancini.
The Phillies left the potential tying and go-ahead runners on base and were 1-for-their-last-22 with runners in scoring position.
Pressly struck out Hoskins to open the ninth and Realmuto flied sharply to center field. Pressly hit Harper with a pitch to put the potential tying run on base with two outs.
That brought up former Cincinnati Reds outfielder Castellanos. Pressly quickly jumped ahead 0-and-2, then threw straight balls to run the count full, then retired him with 88 mph slider, sending the teams to Houston for Game 6 on Saturday night.