The rookie hit a tiebreaking homer in the seventh inning and the Rays once again rallied from an early three-run deficit, beating the NL East leaders 4-3 Sunday.
"This is a morale booster," Tampa Bay starter Chris Archer said. "These past few games we've played, we've been playing really, really well. As a whole, we're starting to find it."
For the second straight day, the Rays quickly fell behind 3-0.
Shaffer's third hit in three at-bats against Bartolo Colon (10-11) was a solo shot into the left-field seats. Shaffer entered with one hit -- a homer -- in seven at-bats this season.
"It was awesome," Shaffer said. "My dad is from Cleveland. He's a Cleveland Indians fan, and he's a big fan of him. Getting to face him, it's been pretty cool."
John Jaso drove in three runs for the Rays, who reached the .500 mark at 56-56.
"Overall team wins the past two days," Tampa Bay manager Kevin Cash said.
The Mets have lost two straight following a seven-game winning streak. They did go 4-2 on a road trip that also included a stop in Miami.
"It was a good road trip," Mets general manager Sandy Alderson said. "It could have been a great road trip, but this team played us well."
A day after the Mets scored three runs in the first inning, they got three in the second when Archer lost his control.
Jaso hit a sacrifice fly in the third and added a two-run double in the fifth that pulled the Rays even at 3.
Archer gave up three runs, four hits, four walks and struck out 10 over six innings. All the walks and eight of his strikeouts came in the first three innings for the All-Star.
New York struck out 28 times over the past two games.
"When you face good pitching, our lineup is going to strike out," New York manager Terry Collins said. "We're designed to hit homers, and guys who hit home runs strike out. I'm a little concerned about (28)."
The Rays are 33-30 in games decided by two or fewer runs this season.
Rays: CF Kevin Kiermaier (right thumb) was out of the lineup, but was a pinch-runner in the seventh. "Tried swinging a bat, but didn't have a whole lot of feel," he said. ... C Curt Casali, hit on the left Temple Saturday on a back swing by Mets C Travis D'Arnaud, is fine. "It comes with the position," Casali said. D'Arnaud texted an apology to Casali.
Colon is just one of five active players -- joining Alex Rodriguez, LaTroy Hawkins, David Ortiz and Torii Hunter -- who made their major league debuts before the Rays played their first game in 1998. The 42-year old Colon pitched the 18th game at Tropicana Field on May 12, 1998.
Rays SS Asdrubal Cabrera had his 11-game hitting streak and a stretch of six straight mulithit games both end. ... Colon had his majors-best 13th start without giving up a walk. It's the most by an NL pitcher in his team's first 111 games since Atlanta's Greg Maddux in 2001. ... Colon is 0-5 in his last eight starts against Tampa Bay and 9-6 overall.