Three-time Champions League winner Casillas was a surprise omission having appeared in Porto's two previous Group G matches and all eight of his side's domestic fixtures.
And the change proved costly when Sa, a former Portugal youth international, failed to hold Bruma's shot in the lead-up to Willi Orban's opener for Leipzig.
The 24-year-old improved after half-time and Conceicao claimed he would not deviate from the decision if he had his time over.
"I put out the 11 players I thought were best suited for tonight's game," Conceicao said at his post-match news conference.
"I would not change the decision if I had a chance to make it again. I am paid to make decisions and tonight I put out what I felt was my strongest side."
Porto were made to pay for sloppy defending in an all-action first half and ultimately left themselves with too much to do in search of a second successive Champions League victory.
The Portuguese side are now third in the group ahead of the return fixture against Leipzig, who are five points off leaders Besiktas.
"We failed to keep things tight before the break and made defensive mistakes that we do not normally make," Conceicao said.
"We have two games at home remaining in the group and one away. The home game with Leipzig will be vital to us."