After spending all of 1964 with the triple A Buffalo Bisons, Jones made the Mets out of Spring training and was in the 1965 season opener against the Los Angeles Dodgers.

His batting average dipped to .246 in 1967, and he ended up sharing playing time in center field with Larry Stahl.

Following the season, the Mets acquired Jones' childhood friend Tommie Agee from the Chicago White Sox.

Jones was batting .341 with ten home runs and 56 RBIs in the first half of 1969 earning the starting left field job for the All-Star Game.

[11] The Amazins found themselves in second place, five games back of the Chicago Cubs in the newly aligned National League East when the Houston Astros came to Shea Stadium for a July 30 double header.

[16] On August 22, 2009, following pre-game ceremonies honoring the 40th anniversary of the "Miracle Mets", Jones discussed the incident during SportsNet New York's telecast of that night's game.

Jones said he reminded Hodges of his leg injury, and that the conditions on the field made it difficult for him to play his best.

Jones batted a stellar .429 in the Mets' three game sweep of the Atlanta Braves in the 1969 National League Championship Series.

With the Mets leading 5–3 in the ninth inning, Orioles second baseman Davey Johnson hit a 2-1 fastball which Jones caught near the warning track to win the World Series.

In the top of the 13th inning, with Richie Zisk on first, Dave Augustine hit what appeared to be a home run over the left field wall.

The Mets won the Eastern Division title on the last day of the season with a record of 82-79 but went on to demonstrate that it was no fluke when they upset the "Big Red Machine" in the National League Championship Series.

Police officers found him asleep in a station wagon with 21-year-old Sharon Ann Sabol, who was charged with possession of marijuana.

Jones said he did not know Sabol, but was giving her a ride home in a friend's borrowed station wagon, which ran out of gas, and that he had fallen asleep fully clothed, except for his shoes, waiting for help.

In 1981, Jones was hired by Frank Cashen of the New York Mets to play a key role as a minor-league hitting coach.

Jones helped shape the careers of future Met stars, including Kevin Mitchell, who figured prominently in the 1986 World Series Championship.

In June 2012, Jones was selected as the Mets' "All-Time Leftfielder" by a panel of sports writers and broadcasters, an honor which he said "means a lot to me."

[29] The hip-hop duo The High & Mighty mention Jones in their song entitled "B-Boy Document '99.

"[citation needed] Men in Black 3 features a scene that re-enacts a few moments of the 1969 World Series, which mentions Jones, and depicts his catching of the fly ball off the bat of Davey Johnson that ended the Fall Classic.

[30] Jones' autobiography Coming Home: My Amazin' Life with the New York Mets was published in August 2022.