The Grecians missed a stack of chances in the second half as Oxford held on to the lead given them by Steve Basham in only the seventh minute. It was Basham's third goal of the campaign.
United's leading scorer of last season pounced in only the seventh minute, and try though they might, Exeter couldn't pull the goal back.
It left Jim Smith's team with 22 points out of 24 - Oxford's best start to a season for 50 years.
Another 6,000-plus gate was testimony to the club's revival under Smith and chairman Nick Merry.
The victory might have been more comfortable but Oxford missed a penalty for the second match running.
Basham had seen his spot kick saved at Morecambe last Saturday and this time it was Barry Quinn who was holding his head after his first-half penalty was saved by City keeper Martin Rice.
Exeter, who had a good recent record at Oxford, made a very positive start, forcing a corner in the opening 15 seconds, when Matt Day had to clear under pressure, and then going close to scoring.
Lee Phillips met Billy Jones's flag kick from the right with a glancing header which drifted just wide of the far post.
But the U's gradually got their act together, and with their fans singing "we are top of the league", they took the early lead their supporters wanted.
Andy Burgess was the creator with a deft defence-splitting pass which released Basham through the middle, and he coolly rounded the keeper before slotting in.
The Grecians looked for an immediate response, and right back Dan Woodards cut in to fire a low left-foot shot goalwards, but Billy Turley saved comfortably.
Burgess then missed a glorious opportunity to make it 2-0 by driving over from 12 yards out after City's defence headed out Rufus Brevett's cross.
Exeter came forward with confidence against a reshuffled Oxford defence missing skipper Phil Gilchrist, who had to drop out because of an Achilles injury.
But a superb strong tackle from Quinn typified their determination to protect Turley.
The home side had one alarm when a deep left-wing cross by Jones landed inside the six-yard box before being despatched for a corner.
But Smith's side, wearing all yellow for a change at home, continued to look the more dangerous breaking forward.
Basham, his self-belief lifted by the goal, had the confidence to try his luck from 30 yards, and the shot was fierce enough to bring a good save at full stretch to his right from Rice.
In the 20th minute, Marvin Robinson won a penalty for the second game running, but for the second game running it was squandered.
Robinson went over the leg of Chris Todd after good link-up play between Rufus Brevett and Basham.
Todd was booked for the foul and had to leave the pitch injured soon after.
Quinn hit the spot kick firmly, but Rice saved smartly to his left.
Exeter pressed hard at the end of the first half, with Woodards screwing a shot wide after a jinking run, and Jon Challinor seeing his long-range drive deflected for a corner.
United replaced Hutchinson with John Dempster for the second half and the former Scotland Under-21's accurate passing strengthened the home side in the middle of the park.
Former QPR and West Ham defender Brevett, who was making his home debut for Oxford, delivered an outstanding cross from the left touchline and Robinson met it with a bullet header, but Rice arched back to tip it over the bar.
Midway through the second half, however, City missed a golden chance to level. Turley could only parry Challinor's powerful shot from outside the box, and Adam Stansfield, one of two Exeter players facing a near-empty goal, blazed the rebound over.
The U's had to defend desperately in the closing minutes as Exeter applied strong pressure.
Turley tipped over a long-range drive and Challinor missed another gilt-edged opportunity for the visitors by heading across the face of the goal from four yards out at the back post.