Mark McGhee described the loss of a decisive goal in time added on against St Johnstone as "soul destroying".
The Motherwell manager urged his players to recover quickly from the set-back, having led for a spell.
Saints counterpart Tommy Wright though was relieved that his side ended a run of seven league games without a win.
"It wasn't a pretty game, but we got the all-important winner late on and that shows the character of the team," Wright told BBC Scotland.
Motherwell were looking to build on the 3-0 win over Dundee United in midweek that moved them from second bottom to eighth in the Premiership.
The league is so tight that a win at McDiarmid Park would have moved them level with St Johnstone, but instead the home side returned to the top six after gathering all three points.
There was little between the teams. The pitch was bobbly, the occasion was nervous and edgy, and the outcome was two sides who worked hard but carried little attacking threat.
Motherwell - who withdrew Scott McDonald from the starting line-up after he felt a tightness in his hamstring - opened the scoring through Louis Moult.
David Wotherspoon equalised before half-time and the two sides effectively cancelled each other out before Saints' Tam Scobbie headed home Simon Lappin's free-kick in the 90th minute.
"I'm really proud of the players," said Wright. "It wasn't a great run that we were on, and to go 1-0 down again, everybody around the ground is edgy, but we did great to get back in it.
"We're disappointed with the goal that we conceded. They did show a lot of character to get back into it and to go in at 1-1 at half-time was a big help to us. At 1-0, with the crowd on their backs a bit, it would be have been easy to fold, but they didn't.
"Sometimes it's percentage football that teams are playing and that means chances are maybe at a premium. We were more positive than we have been in recent weeks in the last third and I'm delighted they kept going.
"I've total belief in the players to finish the season strongly. This time last year we were 11 points off Dundee United in fourth place and we ended up fourth. They're capable of it."
McGhee was frustrated after his side conceded a last-minute goal for a sixth time in recent weeks. He felt his players had performed well enough to earn a point from the game, but stressed that they need to hold their nerve at a crucial time in the season.
"The performance was good on a dreadful pitch to play on," McGhee said. "We played the conditions, it was energetic, everything I hoped for.
"We didn't get a second goal, which was disappointing. Not a lot of end product, of course, but a disastrous outcome. But we regroup and we go again next week.
"People are tired, [St Johnstone] take risks and put everybody in the box, one of them gets their head to it and we end up losing a goal. We didn't deserve to lose and we shouldn't have lost.
"The defeat against Kilmarnock didn't see us capitulate in any way, we went to Dundee United and did well and won the game. Today we should have got something from the game, we didn't. Get over it and go on to the next one."