Clemens came off the bench in the second half and engineered two third-quarter touchdown drives against the Giants' backups to lead the Jets to a 20-12 victory on Saturday night in the annual preseason game between the New York rivals.
"With each game that I have a chance to play in, and with each rep I get in practice, I'm growing in confidence and I think the offense is as well," Clemens said after completing 6-of-8 for 122 yards and an interception. "Any time you get some experience it is a good thing."
Jets coach Eric Mangini said both quarterbacks did some things well, as did cornerback and top draft pick Darrelle Revis, who was impressive in his NFL debut.
"It's been pretty vanilla here in the preseason and that's just the approach we have been taking," Mangini said.
The Jets (2-1) scored twice in a little over four minutes to take command. Danny Ware had a go-ahead 16-yard touchdown run and Clemens completed consecutive passes of 45 and 34 yards before scoring on a 1-yard sneak.
Pennington combined with halfback Leon Washington on a 79-yard catch and run for a touchdown on a stunning first play from scrimmage, but he and the offense failed to record a first down the rest of the half.
"I feel good physically," said Pennington, who was 5-of-11 for 89 yards. "I feel good mentally. We're just inconsistent."
Take away the opening TD pass, and Pennington was 4-for-10 for 10 yards. He has one touchdown pass and two interceptions turned into opposition touchdowns in the preseason.
Manning and the Giants (1-2) dominated early, controlling the ball for more than 21 minutes in taking a 12-6 lead.
It was perfect timing for Manning, whose leadership was criticized by former teammate turned football analyst Tiki Barber on the Sunday Night Football halftime show this past week.
Manning responded with a ripping criticism of Barber on Tuesday, and he followed that up with another solid performance against the Jets.
When asked about the controversy with Barber, Manning feigned ignorance.
"I am just trying to go out there, play well and put our team in situations to win," Manning said. "We are doing a good job offensively. The mistakes we are making are correctable."
Playing without Plaxico Burress (ankle) and Pro Bowl tight end Jeremy Shockey (hamstring), Manning hit 17-of-25 passes for 146 yards. That included a 5-yard touchdown to free agent Anthony Mix late in the first half to put the Giants ahead 12-7.
"I think you guys made more a big deal about that than we did," Giants guard Rich Seubert said of the Manning-Barber controversy. "Eli is a leader. Everybody leads differently. Everybody in this locker room has Eli's back. He's our quarterback."
The lead could have been bigger had veteran Lawrence Tynes not missed field goal attempts of 40 and 42 yards in the half. He converted on a 40-yard attempt.
Free agent Josh Huston, who is battling Tynes at kicker, also missed a 42-yard field goal attempt in the fourth quarter.
"Too many opportunities on the field were left out there," Giants coach Tom Coughlin said. "We missed too many field goals. We had the ball on the 25-yard line three or four times and came away with no points."
Pennington's touchdown pass to Washington came on a play in which the halfback went in motion. Cornerback R.W. McQuarters bit on a pump fake and Pennington found Washington in stride. He scored after making safety James Butler miss a tackle near midfield.
The Giants limited the Jets to 66 first-half yards. That changed after Clemens took over against the second-team defense.
Ware put the Jets ahead 13-12 by carrying on six straight plays during a 44-yard drive.
The next time the Jets got the ball, Clemens hit Justin McCareins for 45 yards on the first play and Brad Smith for 34 yards on the next. That put the Jets at the 1-yard line, and Clemens followed his line into the end zone for the touchdown on the next play.
"It was a good time to call it," Clemens said of the first long pass. "I'll tell you what, Justin hit fifth gear to go get that ball."
The Giants again played without Pro Bowl defensive end Michael Strahan, who is holding out while he decides whether to retire or to return for a 15th season. Justin Tuck replaced him at left end and had a sack.
Giants linebacker Kawika Mitchell left the game in the first half with a groin injury.