Second-half goals from Nicky Low and Niall McGinn earned the Dons their second victory in the Scottish Premiership this season.
McInnes said: "We anticipated a tough match against a difficult opponent. After the first 10 minutes I thought we did very well but at half-time we were possibly ruing the fact we hadn't scored.
"We were really happy with how we were mixing our play up, and with the tempo and we asked them for more of the same after the break."
McInnes was delighted with the quality of Low's goal that broke the deadlock, but had even higher praise for McGinn's strike.
He added: "Nicky brought a wee bit of quality to the game with his goal and then Niall bettered it with an outstanding finish.
"They were two real quality goals, but we had enough throughout the rest of our play for me to be pleased with. I'm really pleased for the boys."
Due to the international break Aberdeen's next game against Celtic is a fortnight away and McInnes emphasised the importance of recording a win before the break.
He said: "It can be a difficult two weeks if you haven't won your last game. We know there's a lot of work ahead of us and areas we can improve."
Thistle manager Alan Archibald admitted his side had only themselves to blame for the defeat.
He said: "It was a decent goal but from our point of view, there wasn't enough pressure on the ball and it was the same story with the second goal. We stood off them and let them play.
"Our ball retention was very poor as well and we spoke about that at half-time and then went out and shot ourselves in the foot.
"We brought our problems on ourselves. Aberdeen were the better side, there's no doubt about that. I was disappointed that we didn't get in their faces more.
"We know Aberdeen have got good quality from middle to front. If you let the three guys behind the striker play, they'll cause you problems and we saw that with the two goals."