Goals in each half from Fraser Hornby and skipper Ross McCrorie and a resolute defensive display saw the young Scots move a point behind the Czechs in Group 4 with a game in hand at San Marino to come next week.
Gemmill's side finish their group campaign next month with games against Croatia and Greece, who are both a point behind Scotland and play each other next week.
But the former Scotland midfielder is focused on the trip to the enclave inside Italy after losing skipper McCrorie to Steve Clarke's senior squad.
Gemmill, who left Celtic midfielder David Turnbull on the bench at Tynecastle, joked: "I might treat myself to a look at the table now.
"But my only focus now is how are we going to beat San Marino because we are going to have a lot of players missing again and Allan Campbell is now suspended and Ross McCrorie is moving up to the full squad so we will have to pull some players in.
"It was so rewarding to see the players execute the game plan. I feel they are a very good team and they showed that so I am so proud that we shut them out and contained them.
"The mentality, intelligence, understanding and crucially, the willingness of the players to do the work was fantastic.
"You also have to factor in we had eight players missing and that was a very young squad, so it really has been a great night."
Reading defender Tom McIntyre and Lewis Mayo, who is on loan at Dunfermline from Rangers, were commanding in central defence as Scotland denied the Czechs many clear openings despite their pressure.
Gemmill said: "George Johnston couldn't come - he wasn't allowed out of his country because a Feyenoord player tested positive, so he was in isolation.
"So that gave an opportunity to Tom and Lewis to come into play and they were excellent. To do it on that stage against that level of opposition then I think they deserve a lot of credit.
"The goals were excellent too and that was part of a really great performance."