The 4-2 success stretched the Iron's unbeaten run to four games following three consecutive draws.
"Before the start of the season, if somebody had asked me if I would be happy with just four defeats in our opening 16 games then the answer would have been yes," said Knill.
"But it's nine draws in those games which have been frustrating. We have played well enough to have won in most of them and it's learning to turn those sort of games into three points which is going to be key for us.
"The victory we had makes the points we have taken from our previous three draws even better ones. But it was certainly a game of two halves and we were quite happy to come in at the interval on level terms.
"It would have been harder for us had we come in behind. But in the second half we tried to play in Tranmere's half instead of allowing them to play in ours and that proved the difference."
Tranmere twice took the lead through Mustafa Tiriyaki - a player who failed to win a deal after a trial at Glanford Park in the summer - but were pegged back through goals from Shane Duffy and Bobby Grant.
Chris Dagnall put Scunthorpe ahead before Grant converted a penalty to make the win safe.
Les Parry, the Tranmere boss, criticised the referee Robert Madley - who sent off Rovers midfielder Jose Baxter for a foul on Sam Togwell and awarded a penalty after Michael O'Connor went down in the area following a challenge from Ian Goodison.
"The game changed on the sending off decision. I thought generally the referee had a poor game. I cannot criticise him on the major decisions because I was too far away. But I can be critical of his decisions leading up to those two major incidents," he said.
"Just before Baxter was sent off there had been a couple of bad challenges gone in. If players are allowed to get away with those then injuries can be caused.
"Before the penalty award against Goodison he virtually had his shirt ripped from him by one of the Scunthorpe players."