Albion had to overcome the shock of falling behind to a 12th-minute opener from Jamie Mackie before a strike from Shelton Martis and a double from Marek Cech - his first goals for the club - moved them onto 14 points from six games.
Di Matteo said: "It was hard work. At the end, the result may have looked comfortable but it was a hard game for us.
"Plymouth came out of the blocks really well and we had to change a few things around.
"But getting the equaliser and a second goal before half-time was important and we were better in the second-half.
"We are top of the league and we will enjoy that. We are also still unbeaten and we will enjoy that as well.
"We have our philosophy of how we want to play and we can score from anywhere in the team, which is important.
"We are going in the right direction and I think the chairman is very happy that we are unbeaten."
While Albion are top of the table and flying, Plymouth boss Paul Sturrock was left downcast after again seeing his side undone by a poor defensive display.
Plymouth are without a win this season and have collected only two points from a possible 18.
Sturrock, whose side changed their strip at half-time from white to green after struggling to pick each other out, said: "Until we lost the second goal we did very well.
"I am going to use a phrase I have used for the last six games and that is, 'if only'.
"But we can't keep saying, 'if only'. We are losing bad goals and Paul Sturrock prides himself that his teams are normally hard to score against.
"The first goal came from a corner and we spent 45 minutes working on defending them in training on Friday and my worry now is that it is playing on the minds of the players.
"We have lost too many from set-pieces. We just need a wee break because at 2-1 down we hit the bar.
"The important thing for us is that we get just three points from somewhere even if it is with the worst performance of our lives and the ball goes in off someone's backside. That is all I want."
Plymouth initially stunned Albion when the impressive Alan Gow sent Mackie clear.
Mackie easily brushed aside the challenge of Shelton Martis and powered forward from the edge of the area.
The angle at the near post looked too acute but he somehow slid his weak shot under goalkeeper Scott Carson from two yards.
Plymouth should really have doubled their advantage in the 22nd minute when Gary Sawyer headed wide from close range and that proved to be a costly miss as Albion dragged themselves back on to level terms through Martis 12 minutes later.
He had the simple task of pushing the ball into an empty net after Plymouth goalkeeper Romain Larrieu failed to collect a corner from Graham Dorrans.
Albion were a different proposition after parity was restored and they were rewarded for a spell of intense pressure when Cech gave them the lead in spectacular style five minutes before half-time.
Roman Bednar neatly flicked the ball into the path of Cech and the Slovakian international left fly with a fierce 25-yard drive that whistled past the helpless Larrieu for his first goal since his £1.4million move from Porto last summer.
Plymouth were inches away from an equaliser when Karl Duguid hit the bar in the 52nd minute and again when Carson tipped Cillian Sheridan's header over the bar.
But Cech sealed Albion's success with a neat finish from eight yards when he converted a cross from the hard-working Dorrans.