Howard sent a 3-1 pitch from Vidal Nuno to deep right before Byrd drove an 0-2 offering over the center-field fence.
Derek Jeter had a hard single in three at-bats. The Yankees captain has struggled offensively, going 6 for 47 (.128) in 16 games.
Jeter was limited to 17 games last season after breaking his left ankle in the 2012 playoffs.
Phillies: Jeff Manship allowed five hits in four shutout innings.
Yankees: Warren gave up two walks and had one strikeout in a scoreless inning. Phelps pitched the second, allowing Bobby Abreu's RBI single after consecutive errors by third baseman Kelly Johnson.
Both Phelps and Warren are expected to work out the bullpen.
''Disappointing, but I still have a chance to help the team,'' Phelps said.
Phillies: Infielder Freddy Galvis has been released from the hospital after getting four days of treatment for a MRSA infection in his left knee. He will start the season on the disabled list.
Abreu returned after missing a couple days with left shoulder soreness.
Reliever Mike Adams allowed two hits during a scoreless fifth in his first big league spring training game. He is coming back from a shoulder injury.
Yankees: Center fielder Jacoby Ellsbury went 1 for 4 with two walks as the designated hitter in a minor league intrasquad game. He had missed the past 1 1/2 weeks due to right calf tightness, and could play defense in a minor league game Wednesday.
''Today was the first step in the sense of just playing in the game,'' Ellsbury said. ''I've been running, sprinting, doing all that stuff.''
Ellsbury expects to be ready for opening day.
Infielder Brendan Ryan, out with upper back spasms, says he will start the season on the disabled list. Dean Anne and Yangervis Solarte could replace him in the backup infield role.
Phillies: Infielder Ronny Cedeno was released, leaving Cesar Hernandez and Reid Brignac as internal options to be backup infielders.
Infielder Kevin Frandsen, outrighted to Triple-A Lehigh Valley Sunday, opted for free agency.
Catchers Cameron Rupp and Sebastian Valle were sent to the minor league camp. Catcher Koyie Hall was reassigned to major league camp as a non-roster invitee.
Yankees: Catcher John Ryan Murphy was sent to the minor league camp. Francisco Cervelli has become the clear favorite to backup starting catcher Brian McCann.