Midfielder Adam Bolder had struck twice to give the Hillsborough side a surprise lead, before a Richard Wood own goal and Beattie's last-gasp strike left honours even.
It was a valuable point for Wednesday, who won 2-0 at Hillsborough in January in their fight against the drop and the result ends United's hopes of a top-six finish.
Billy Sharp almost got an early breakthrough, finding space on the left flank to lash in a swerving strike that was snapped up by Lee Grant as Beattie tried to connect.
The Bramall Lane side pressed again, midfielder David Cotterill drilling in a teasing cross which was cleared by Grant to the waiting Michael Tonge, who ballooned the ball high over the target.
Wednesday, with one defeat in 11, but too many drawn games, were in trouble again after conceding a free kick 30 yards out, Tonge stroking the ball to Gary Speed, whose stinging low strike was scooped up on the line by Grant.
Sharp almost broke the deadlock in the 25th the little striker trying to catch Grant off his line with a delicate chipped shot, the Wednesday keeper producing another vital stop as her finger tipped the ball over the bar.
The pressure was relentless, but defiant Wednesday refused to cave in and stunned the home fans six minutes before the interval.
Midfielder Steve Watson, playing in an unaccustomed role of full-back, broke down the right wing as the United defence backed off, his teasing cross finding on loan QPR midfielder Bolder whose angled header flashed past Paddy Kenny.
Wednesday snatched a second in the 54th minute, the tricky Franck Songo'o weaving past Derek Geary to drill in a low cross, Kenny could only palm the ball into the path of Bolder, who finished from close range.
United pulled one back in the 61st minute, Sharp's close-range shot was blocked by Grant, the ball hitting centre-back Wood and spinning over the line.
Beattie grabbed the equaliser with a stunning free-kick from 25 yards into the top corner in the 86th minute, his fifth goal in three games.