Johnson is in his fourth season with the Chiefs after signing from Coventry whilst Thomas is currently in his second full-time stint with the Chiefs having previously featured for Bath, Bristol and Gloucester.
"Obviously this is very positive news for the club that we already have got players who are prepared to commit to the club over the long term", said head coach Rob Baxter.
"Both Tom and Haydn have played a big part in what we have done so far this season in the Premiership and they can see that we are a progressive club who are looking to move forward all the time.
"It is decisions like this that demonstrates that players want to buy into what we are trying to achieve here. I'm delighted that both the guys are willing to be part of what we want to achieve in the long term."
Thomas, who scored a try in his side's 34-19 victory over Bourgoin in the last round of the Amlin Challenge Cup is delighted to have signed his extension.
"I am very pleased to have signed on for a further three years. Exeter is a fantastic club and I want to be part of its future", he said.
"Being here it's such an enjoyable place to be around, I really enjoy it, and I don't really see any reason why I would want to leave.
"The coaching staff and set up is brilliant - on top of that you have Paddy [Anson] and his team on the conditioning side - they are all on top of their game. At the same time, you're living in Devon and where else would you want to be?
"I am really enjoying my rugby this year in the Premiership and I feel we are really achieving something. From the very top with the likes of Tony Rowe, the directors, Rob [Baxter] everyone is pushing in the right direction and I just wanted to part of that."
Next up for Exeter on the European front is back-to-back fixtures against compatriots Newcastle Falcons, the first game taking place on Saturday December 11.