Upton pointed a finger in Longoria's face after the third baseman questioned the center fielder's effort in the fifth inning Sunday, when Gerardo Parra hit a two-run homer that helped give the Arizona Diamondbacks a 2-1 win over the slumping Rays.
Rodrigo Lopez and three relievers combined on a two-hitter for the Diamondbacks, who took two of three from the Rays. On Friday night, Edwin Jackson no-hit Tampa Bay, which had seven hits in the series.
"It's a byproduct of a frustrated team," Longoria said. "We're trying to win games and guys are going to have differences of opinion. I just wanted to know what was going through his head. The bottom line, we've talked about it and it goes no further than today."
Longoria was upset with how Upton positioned himself and went after Rusty Ryal's drive that ended up a triple in the fifth, ahead of Parra's homer. Several teammates stepped in between the two, and Willy Aybar wrapped his arms around Upton while separating the teammates.
"B.J. came in off the field after that particular play and everybody saw it, and some guys were not really pleased and certain things were said," Rays manager Joe Maddon said. "He was set up on the other side -- in other words a right-handed hitter he set up in right-center field and the guy pulled it into left-center. He just did not run as hard as he possibly could have after the ball, that was obvious. That one there just didn't have a good look to it."
Added Maddon: "It's just one of those moments that happened and now it's up to me to handle it properly."
Maddon planned to meet with Upton, and was undecided about any potential punishment. Upton, who was also picked off first after a walk in the bottom of the fifth, has been benched several times for a lack of hustle.
"A little run in," Upton said. "It's done with and move on."
Upton thought left fielder Matt Joyce might get to the ball based on their positioning.
"Maybe I should have cut it off, but it's over with now," Upton said.
The Rays are 12-19 since May 23, dropping from first to third place in the AL East.
"We're not hitting, period," Longoria said.
After Joyce walked with two outs in the ninth, Upton hit a drive that was caught at the center field fence.
"The ball ran out of gas at the last second," Arizona center fielder Chris Young said. "When he swung the bat and made contact, I thought he was the hero."
Parra hit his second homer of the season off Wade Davis (5-9) to put Arizona up 2-0. Davis gave up two runs and four hits over 7 1/3 innings, and is 0-5 in five starts during June.
The Diamondbacks have only three wins in their last 19 road games.
"You come into this place against a good team and get a series win, it's time to get out of town and go onto the next city," Diamondbacks manager A.J. Hinch said.
Carlos Pena had an RBI double in the sixth to make it 2-1.
Ben Zobrist hit a two-out liner with Longoria on third in the bottom of the fourth that hit Lopez on the left forearm. Lopez recovered to threw Zobrist out at first.
In the first meeting between brothers, Arizona's Justin Upton got the better of B.J. Justin Upton went 5 for 9 with a homer in the series, while B.J. was hitless in nine at-bats.
Jackson, who threw 149 pitches and walked eight Friday in his no-hitter, will have his next start pushed back from Wednesday to Friday or Saturday. ... Rays LF Carl Crawford (sore left shoulder) was out of the lineup for third straight game, but did pinch run in the eighth.