The Tynecastle team conceded their first goal in the SPL in 494 minutes when they allowed managerless Well to equalise just a minute after taking the lead at Fir Park last night.
However the Jambos showed great guts to restore their advantage and close the gap on second-placed Celtic in the SPL to just three points.
Jefferies was delighted with the application and attitude shown by his players and smiled: "I'm annoyed that we lost a goal! It's just typical, one minute after we scored Marius should have put the ball into Row Z but he has tried to keep it in play and not caught it right and it has fallen to their midfield player, who was out of position and they have gone through the gap.
"That was a bit annoying but we should have been ahead before we scored in any case, I don't know how Stephen Elliott has missed that one under the bar after a great ball in from Temps.
"But what was great about last night was that we made the better chances, there's no doubt about that. Again, Stephen Elliott should have put us in front before we got the penalty kick, then Temps had another good shout for a penalty. With the first one having been given, I thought that the second one might have been given as well."
Jefferies admitted he was pleased to come away from Lanarkshire with all three points in the bag following a dismal run of results, both home and away, against the Steelmen last season.
Hearts lost three of their league clashes with Motherwell in the last campaign, picking up just three points from their four league meetings in 2009/10 and Jefferies added: "Motherwell are a good side and they actually played quite well last night. It's great that we could come and get the win, especially when you consider that we lost a couple of boys just before the game.
"We've had to adjust to that and we have come to a place where we don't have a good record. They're a good team, they're difficult to beat at Fir Park and yet we have come out on top.
"To do that just goes to show the improvement in our side and I think that we took it up another notch last night."
This might have been a clash between third and fifth but the first half didn't offer too much in the way of entertainment.
A weak effort from Kevin Kyle fell straight to the feet of Ryan Stevenson in 12 minutes but the former Ayr man couldn't keep his shot down and the ball fizzed just over Darren Randolph's crossbar.
Rudi Skacel then tried his luck from distance but again missed out by just a matter of inches, his shot flying past the keeper's right-hand post.
Their best chance came just before the half hour with a cracking ball in from David Templeton but Stephen Elliott somehow headed over when he was almost under the bar.
Hearts got their reward though a couple of minutes before half-time when Kyle did well to win possession on the by-line. The striker managed to pick out Templeton in the centre and the youngster's audacious overhead kick caused all sorts of problems for Well, Randolph twice getting his hands to the ball but there was nothing he could do as it came off Mark Reynolds and into his own net.
However, the Jambos could only hold onto their lead for a matter of seconds before Alan Gow's cross was poked low into the net beyond Marian Kello by Keith Lasley, forcing the Hearts keeper to pick the ball out of the net for the first time in 494 minutes.
After the break Tom Hateley produced a brilliant tackle to deny Elliott what looked a certain goal after Skacel and then Kyle had led the charge up the pitch.
Darren Barr, who was back in the side after Eggert Jonsson was ruled out by illness before kick-off, almost teed up a second for Hearts when he found Elliott, who steadied himself before unleashing his shot, only to see it come crashing back off the underside of the bar.
Just before the hour though, Hearts got the winner they deserved, although it came from the penalty spot after Stephen Craigan had brought Templeton down.
Kyle, who is due to become a father again any day, smashed the ball home from 12 yards to the keeper's left to give the Jambos the points.
To compound the home side's misery, they were reduced to ten men when Steve Jennings was shown a bizarre straight red card for what appeared to be simply touching the referee on the shoulder.
Motherwell's caretaker manager Gordon Young couldn't shed any more light on that incident, which came in the aftermath of a Well claim for a spot kick being waved away. He said: "I thought that we suffered for not having played in the last two or three weeks but we got back into the game just before half-time and the feeling in the dressing room was that we could build on that.
"Unfortunately, we didn't manage to kick on from there. Obviously, losing the penalty wasn't ideal and I thought that we looked a bit leg weary as the game went on. I have to try to galvanise the team for the weekend now. Getting the goal back so quickly gave us a great opportunity because I thought that we passed the ball a lot better.
"Motherwell's game plan is all about playing combination passing and trying to move the ball through the middle of the park in an offensive manner and we had to overcome ~the long-ball game that Hearts play - and the dominating fashion that they do so. I felt that we coped with that reasonably well and to go in at half-time level gave us a real chance but we just couldn't take it."