Henderson, who missed a week because of an injured right hip, singled and scored the tiebreaking run on John Olerud's single in the seventh inning as New York beat San Diego 4-3 to end its three-game losing streak.
Henderson joined the crowd of 32,101 in saluting Gwynn when the 3,000-hit man came to the plate in the first inning. Gwynn tipped his helmet as Henderson took off his glove in left field to applaud.
The two players visited before the game, and the 39-year San Diego star surprised Henderson with a prediction.
"He said I'd be the next one to 3,000," Henderson said.
Henderson got two hits, giving him 2,761 lifetime. Gwynn went 2-for-5, but had an inning-ending groundout with the bases loaded in the sixth and the score tied at 3.
Gwynn has 3,006 hits, one behind Al Kaline for 20th place on the career list.
"To see a guy like Rickey Henderson clapping in the outfield and for the fans to give me a standing `o,' it feels real, real good," Gwynn said.
"This is New York and the people here know what's going on," he said. "They only appreciate a visiting player here if they know you're good."
The Mets won despite grounding into four double plays, and overcame three hits by Carlos Baerga in his return to Shea Stadium.
Olerud also had a two-run single and Roger Cedeno tied a team record with his 58th stolen base as the Mets stopped their longest skid since losing eight in a row two months ago. New York remained a half-game behind Atlanta in the NL East.
Cedeno tied current Mets first-base coach Mookie Wilson, who had 58 steals in 1982. But Cedeno also bounced into two double plays he had grounded into just two in 330 previous at-bats this year.
Cedeno stole second base in the eighth inning, and had the actual bag in his locker.
"I want to give it to my mother. Today is her birthday," he said. "The next one, I'm keeping for myself."
The Padres dropped their fourth straight. They have lost 16 of 19, including the resumption of a suspended game.
Henderson singled with one out in the seventh off Andy Ashby (10-6) and was running on Edgardo Alfonzo's single to center, barely making it to third with a head-first slide. Olerud followed with his hit.
"I might be the sparkplug," Henderson said. "The best thing I can do is to go out and create something."
Ashby gave up a career-high 14 hits in seven innings as the Mets rallied from an early 3-0 deficit. He did not, however, permit a home run after giving up Mark McGwire's 500th and 501st homers in his last outing.
"It's frustrating when the offense gets the lead early and then you give it right back to them," Ashby said. "My command was a little off."
Rogers walked a season-high six, including three in the fourth. Rookie Ben Davis blooped a two-out, two-run double and Ashby hit an RBI double for a 3-0 lead, bringing scattered boos from the stands.
Darryl Hamilton singled home a run in the Mets fourth. Rogers singled for his second major league hit in the fifth, made a dive into third on Alfonzo's double and scored on Olerud's two-run single that tied it at 3.
©1999 The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed