Following the penalty call, City's Josh Jonas was given a yellow card for dissent, earning him 10 minutes on the sideline, and Marist managed a second goal while City were undermanned.
"To be fair, to hold them for an hour, I thought we did really well," Francis said.
"They probably had 70 per cent of the ball so for it to be 2-0 - and they are league leaders - I think we did really well."
He said they had their own chances too.
Anthony Bell, who wasn't due to play but had time in the end, was fouled just outside the box in the first half and the resulting free kick from Kyle Graham-Luke was goal-bound before Marist's keeper "made an absolutely fantastic save".
"That would've made a massive difference to the game," Francis said.
"And we had another couple of opportunities in the second half. We've given it everything we've got."
Francis said Thomas Sinton earned man of the match honours for a solid performance in central defence.
The loss means City cannot lift themselves from second to bottom with just one game left in their season which, Francis said, was disappointing because his side had a much better second round of games.
But they still have an opportunity to finish 15 points ahead of wooden spooners Red Sox Manawatu who City play next Saturday.
"We'll just go away and have a bit of fun," Francis said.
