Niese was removed for a pinch-hitter with two outs and a runner on third base in the sixth inning. At the time, the Mets trailed 3-2 after the Brewers had mounted a three-run rally with two outs in the fifth. He had thrown 89 pitches.
"The point is, there's a time when you've got to get your team back in the game," Collins said. "You've got a runner on third base in the sixth inning, even though you're down a run, Jon's got basically one more inning to go anyway. He's at  pitches and he's only going to go 105 anyway. You just can't give up that opportunity to try to tie the game up."
In part, Niese was a casualty of the Collins' unconventional lineup, which had him batting eighth. Had he been batting ninth, he may not have come up in that inning, or the run may have already scored.
"I thought I should've been out there anyway, despite if I was up eighth or ninth," Niese said Saturday night. "Terry makes those decisions. Those are out of my control. I could've went one or two more."
Though pinch-hitter Eric Campbell struck out to end the inning, Collins stood by his lineup and decisions from Saturday's 5-2 loss.
"You can't have a crystal ball. You can't look ahead. You've got to just say, I think this is going to give us our best shot to win the game with this particular lineup," Collins said. "You know he's going to get up earlier in other innings than he normally would.
"The biggest thing, had he been able to get out of that [fifth] inning without a lot of damage done, he would've still been in the game. I go back and say, 'put a cap on it and get us out of this thing and you'd stay in the game.' When you're down a run and you haven't been scoring, we've got to take that chance."
Niese said that he did not express his unhappiness to Collins when the decision was made.
Caitlin Swieca is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.