Manchester United striker Rooney curled home a free-kick 17 minutes from time at the A Le Coq Arena on Sunday in Tallinn to ensure England secured a 1-0 victory that makes it three wins out of three in Euro 2016 qualifying Group E.
Hodgson's side dominated the first half and should have been in front at the break, but were not as impressive in the second half, despite Estonia having captain Ragnar Klavan sent off for a second bookable offence only two minutes after the interval.
Rickie Lambert was poised to come on just before Rooney struck, but Hodgson insisted it was more likely Danny Welbeck would have been hauled off rather than Rooney.
The England boss told ITV: "We were going to put Rickie Lambert on, but we were discussing which player would come off.
"It was more likely to be Danny Welbeck, as Danny went over on his ankle and did come off in the end."
Hodgson felt group leaders England made life difficult for themselves after failing to take what would have been a deserved first-half lead, but was relieved to see his side secure another three points to maintain their impressive form.
He added: "It was hard work.
"We played well in the first half, we played some excellent football without taking our chances and that meant that there was an air of frustration setting in and an air of pressure going out in the second half.
"Everyone was aware that when you have played well you have to take at least one chance.
"Luckily we did that in the second half and it's four wins in a row [in all fixtures], which is not to be sniffed at, and five clean sheets [in a row]."
Rooney now has 43 goals for his country as he edges closer to Bobby Charlton's all-time record of 49, with Hodgson pleased to see his skipper find the back of the net in a game in which he could have had at least a hat-trick.
He said: "It was a good free-kick from Wayne, but it was a frustrating night for him.
"He had a lot of the ball and a lot of chances, I think he'd have been bit disappointed if he'd not have scored. But he scored the winner and we go away with three more points."
