Captain Tommy Rowe scored for the third time in four games to put the visitors ahead on 14 minutes before Tyrone Barnett doubled the advantage.
Rovers have now conceded 13 goals in four League One games and after taking second spot in the table Ferguson admitted his side seized their opportunity.
"Normally Tranmere is a difficult place to come to and the games are always hard here, but we were comfortable this time and it is very rare you get games like this here," he said.
"I was please about the clean sheet and we were very professional in the way we went about things.
"We got ourselves in front and scored two excellent goals before the penalty.
"When they went down to 10 men we made sure we didn't get complacent and we knew we could get more goals.
"I thought we started the second half a little flat but the fourth goal picked us up again.
"We controlled the game and of course goals do change games and we were very clinical in the first half.
"We are pleased to have won four on the bounce in the league but the start to a season is 10 or 12 games so we are not getting carried away."
While Peterborough are flying high, Tranmere, who were in contention for promotion for much of last season until fading, have endured a miserable start with just one point to show so far.
Defeat left Ronnie Moore's side in the relegation zone and while the manager believed Jones' sending off was harsh he was offering no excuses for the result.
He said: "At the start of the game there was nothing in it and then a stupid mistake has cost us.
"We defended just like we have for most of the season and that is one of the reasons I need to bring someone in.
"We need to strengthen defensively but when you go down to 10 men against a team like Peterborough then you will always be up against it.
"Defensively we were awful, shambolic at times. It becomes embarrassing.
"There was a lot going on in the dressing room after the game but we need that on the pitch.
"I didn't really think the sending off was deserved but we haven't created anything.
"We knew it was going to be hard but we need to man up and do it quickly.
"Players need to take responsibility on the pitch. I can't take responsibility for them. It hurts because we have a lot of pride."