Brazil outclassed Serbia in their opening clash as Richarlison's second-half goals sent the five-times champions top of Group G.
"I think both Brazil and Serbia were on equal level in the first 45 minutes, I didn't see Brazil much more dominant at that time," Stojkovic told a news conference.
"We got defeated in the second half, when we literally fell physically, and we were no longer a team -- and of course Brazil knew how to take advantage of this. We simply could not recognise our team."
The Serbia coach stressed his side were not fully fit, including their all-time top scorer Aleksandar Mitrovic who was named in the starting line-up.
"You are well aware of the fact that we came with a lot of problems to Qatar," Stojkovic said.
"We have a lot of injuries to deal with and that is not the right time (for that), especially because it's among the players who are the key players of our team, unfortunately.
"The intensity was really high in the second half, we gave too much space to the Brazilians. But the key point for me is that my team physically was completely down -- so I want to know why, because I don't. This is a surprise for me, something strange.
"Plus I have to repeat. We have three key players injured. It's too much for us. We are not Brazil with 200 million people, we're a very small country. They got injured just before the World Cup so it's really unlucky."
Next up for Serbia are Cameroon, who lost 1-0 to Switzerland on Thursday.
"We need a couple of days to rest as much as possible and there will be no physical exertion. We know what our goal is and we will not give up," Stojkovic added.
"To lose against Brazil is no shame. They are well-deserved winners ... For the next match, we will need to figure out what's the best for us, we need the healthiest players playing."
