Scunthorpe's loss at home to Darlington - for whom former Ipswich and Middlesbrough striker Alun Armstrong struck the only goal of the game - allowed the Glovers to move on to 49 points.
But they are kept off the top spot by the Iron's narrowly better goal difference of +19, compared to +18 for the Somerset side.
Their clash with Swansea at the Vetch Field had threatened to end in a stalemate, but Latvia Andrejs Stolcers hit 12 minutes from time and Phil Jevons hit a second in the last minute.
Although United and Yeovil remain clear at the top of the table, Southend capitalised on Swansea's loss to close the gap to the final automatic promotion spot.
They eased to a 3-0 win over Rushden and Diamonds at Roots Hall, with Northampton also strengthening their play-off position with a 2-1 success over Mansfield.
Trevor Benjamin, who joined on loan from Leicester on New Year's Eve, scored his first goal for the club.
Cambridge remain rooted to the bottom of the Football League after a 1-0 home loss to Boston, while second-bottom Kidderminster earned a point at Orient - but came close to sneaking all three points against the London side.
Shrewsbury's win over Bristol Rovers moves them up to 21st, while Grimsby's game against Rochdale at Spotland was abandoned at half-time due to heavy rain.
Lincoln, Oxford and Notts County beat Bury, Wycombe and Cheltenham respectively.