Kirk Jackson, who joined Yeovil from Stevenage a month ago, got the opening goal as the Conference leaders moved six points clear at the top and left Stevenage in deeper trouble in the relegation zone.
Jackson had almost got the game off to a sensational start, after just 25 seconds he raced down the left and his powerful drive flashed inches wide of the far post with Mark Westhead beaten.
Yeovil certainly looked like champions in the opening 30 minutes, but gradually lost their way and came under the cosh for long spells in the second half.
Jackson's goal came after 26 minutes with Yeovil's first shot on target. Gavin Williams, back after injury, crossed from the right and Michael McIndoe knocked the ball into the path of Jackson who shot home from eight yards.
Almost immediately the Glovers lost their skipper Terry Skiverton with a leg injury but Jimmy Aggrey came off the bench for his home debut and did an excellent job.
Martin Williams, back after injury, was causing Yeovil some problems at the back and he slid Stevenage level on 43 minutes after Roy O'Brien lost the ball on the touchline to Jude Stirling.
Yeovil struck back immediately, however, and right on half time got what proved to be the winner.
A McIndoe free-kick was floated across the box from the left and Colin Pluck raced in with a superb diving header.
Although Stevenage had the better of much of the second half it was not until the 89th minute that they really caused problems for Yeovil. Williams flicked off for DJ Campbell and the substitute should have scored, but Chris Weale spread himself well to make a great save.
Earlier Stevenage had been reduced to ten men when Sam McMahon was sent off for a second yellow card.
Yeovil boss Gary Johnson said: “I was glad to get three points. I don't think for a moment that Stevenage will be relegated.
“Wayne Turner has some good players and he will get them out of trouble.”