Lewandowski had been struggling with a thigh injury he suffered last week in a friendly against Turkey and missed Poland's opening 2-1 defeat by the Netherlands.
He came on in the 60th minute with the game level at 1-1 but could not inspire his team as Austria ran out convincing winners.
"He was fully fit and he has practised with the team," said Probierz.
Poland conceded to fall behind just six minutes after Lewandowski was introduced, then became stretched in their efforts to get back into the match and were ultimately fortunate to not lose by more goals.
"We knew that this would be a highly intensive match and we decided with the medical team and Robert Lewandowski himself that he wouldn't start from the first minute," said Probierz.
"We wanted to get through that Austrian defence in the second half and it's a pity we couldn't score that second goal before them."
Poland will be the first team eliminated from the tournament if the Netherlands fail to beat France in Friday's other Group D match.
