Tomkins, who was out for three months after damaging his knee in England's 30-22 Twickenham defeat by New Zealand in November, paired up with centre Brad Barritt, who did not feature for England against Ireland.
"It's great to see Joel back," said director of rugby McCall.
"In the first 20 minutes we were lethargic. We were a second off in everything we did but then Joel made a couple of important breaks and got us on the front foot."
Barritt, who will rejoin Stuart Lancaster's England squad on Monday, played for 78 minutes before being replaced.
Two powerfully-driven tries from front-row forwards James Johnston and Schalk Brits enabled Saracens to overcome a stiff challenge from the Chiefs.
Both were converted by former England fly-half Charlie Hodgson, who also kicked three second-half penalties
The hard-fought victory keeps Saracens in second place, a point behind Northampton, ahead of Friday night's visit to in-form Bath.
McCall said: "Bath are on a roll at the moment and have been playing some good rugby.
"Their set-piece is very strong and it's going to be a big battle.
"It was a mountain for us to come back from 7-0 down when they had a strong wind in the second half but we dominated the set-piece today."
The Saracens boss added that former England lock Mouritz Botha, carried off during the second half after suffering a worrying-looking neck injury in a tackle, had been taken to hospital "as a precaution but I think he's OK".
Exeter director of rugby Rob Baxter, whose side suffered their fifth successive Premiership defeat after establishing a 10-7 lead after 47 minutes, described the latest setback as "the story of our season".
He said: "We were very competitive for large parts of the game but when the pressure comes on we start to struggle a little bit.
"We scored the penalty which took us into the lead but then we dropped the restart which becomes a penalty and we're struggling.
"From being a team in the lead, with the wind behind us, all of a sudden we found ourselves playing in our own half - but all credit to Saracens. They played the elements exceptionally well.
"I can't fault the players for effort. We had quite a lot of good individual performances out there but it's just some of the decision-making under pressure. We have to keep getting better at it."
- Sports & Recreation
- Brad Barritt