McNeil had missed the past five games with tightness in his right hamstring.
McNeil, who entered the night leading the Mets and third in the National League with a .327 batting average, hadn't played since suffering the injury in last Monday's 6-0 home victory over the Miami Marlins.
McNeil said last week that an MRI showed "nothing" but the Mets were cautious by keeping him out of the lineup.
The National League East-leading Mets also announced Tuesday that sidelined right-hander Max Scherzer (oblique) will make his next rehab start on Wednesday for Double-A Binghamton in a game at Hartford.
Scherzer will be pitching on seven days of rest after his first rehab start with the Rumble Ponies on June 21. Over the weekend, New York dashed speculation that the three-time Cy Young Award winner would be ready to return for Sunday's game in Miami and would start Tuesday for Binghamton at Hartford.
Showalter said the Mets decided Monday that Scherzer should pitch Wednesday instead, citing discussions with Scherzer about how he felt and general caution with the nature of his injury.
"There's no reason to rush it,'' Showalter said. "We're not going to make that mistake.''
The Mets also activated outfielder Ender Inciarte to the active roster on Tuesday and optioned outfielder Nick Plummer to Triple-A Syracuse. To make room for Inciarte on their 40-man roster, left-hander Locke St. John was designated for assignment.
The Associated Press contributed to this report.