Craig Thomson converted a 26th-minute penalty after referee Willie Collum adjudged Steven Saunders to have fouled Ryan Stevenson as the ball came over from a Rudi Skacel corner.
Skacel netted a second after 36 minutes and Stevenson headed in a third after 53 minutes to put Hearts - with Marian Kello back in goal - on course for a comfortable win.
But two minutes after Stevenson's effort, John Sutton headed in a Steve Jones cross and after 60 minutes the striker appeared to get a faint touch on Tom Hateley's free-kick.
Sutton, who has been linked with a free transfer move to Hearts this summer, then headed in an 88th-minute equaliser as Scottish Cup finalists Well completed their comeback.
Having once held a 15-point advantage in the race for third, Hearts now hold a seven-point lead over fourth-placed Dundee United, who earlier today beat Kilmarnock 4-2.
Hearts' pursuit of third place has stuttered in recent weeks and they now have one win in eight games - the March 19 defeat of St Mirren.
The 3-2 victory over the Buddies was Kello's previous most recent appearance and the goalkeeper made a surprise return.
After initially being ruled out by a back spasm, "a private matter" led to his non-selection with manager Jim Jefferies insisting it was a decision he and the goalkeeper made alone, without the intervention of majority shareholder Vladimir Romanov.
Kello showed his value to Hearts just before half-time, having only been called into action after the hosts had established a two-goal lead.
Slippery conditions as a result of torrential rain contributed to a scrappy opening punctuated by Collum's whistle.
After Skacel had a header saved by Darren Randolph and Thomson curled a free-kick over, Hearts were awarded a penalty when Saunders was adjudged to have brought down Stevenson as Skacel's corner entered the area.
Collum had awarded two penalties in Celtic's Scottish Cup semi-final win over Aberdeen last weekend and sent off three Dundee United players in awarding three spot-kicks in their 4-0 loss to Rangers at Tannadice in midweek.
Saunders received only a caution before full-back Thomson scored from 12 yards.
Stevenson hit the post with a shot on the turn after Kello's long clearance up field before Hearts' second came after 36 minutes.
Skacel and Stephen Elliott combined, the latter playing a neat return pass for the midfielder to strike into the roof of the net.
Kello was then called into action, saving a point-blank header from Saunders before spreading himself to save from Jamie Murphy, who was earlier booked for handball.
Hearts captain Andy Webster went off at the interval to be replaced by Adrian Mrowiec but the hosts continued to press forward.
Thomson curled a free-kick over before Stevenson ignored a free Skacel in the middle and struck both posts with an effort from an acute angle.
Stevenson, though, found the net soon after, heading in Santana's pin-point cross from the right to give the hosts a 3-0 lead.
But two minutes later Motherwell pulled a goal back when Jones burst down the right and crossed for Sutton to head in.
Webster's presence in defence was missed once again as Hearts conceded after 60 minutes.
Sutton appeared to get a touch on Tom Hateley's free-kick from wide on the left which went into the bottom corner.
Kello saved a long-range Hateley effort, a Francis Jeffers shot and substitute Maurice Ross' close-range strike as Motherwell's confidence grew.
Jones then saw a left-foot shot come back off the post before Jeffers blazed over after breaching the offside trap to latch onto a long ball.
But two minutes from time the visitors got their just rewards as the hosts' defence was breached once.
Gavin Gunning's cross from the left was met by Sutton, who stooped low to head in beyond Kello and earn a deserved draw.
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