An early John Sutton penalty and a Gary Warren own goal put Motherwell in command at half-time but Graeme Shinnie's 55th-minute effort deceived Lee Hollis and Motherwell survived an anxious second half which culminated in Billy McKay hitting the inside of the post.
Motherwell had secured a Europa League place the previous night and the victory maintains their hopes of leapfrogging Aberdeen when they go to Pittodrie on Sunday.
McCall, who saw most of his first team leave last summer, said: "It's incredible. Twenty-one victories. I said at the beginning of the season Celtic would win it, Hearts unfortunately because of the problems they had would be bottom, and Aberdeen would be second. And that's because they've got such a good management team and a good squad of players. For us to be that near them is beyond what we could have dreamt of, but that's credit to the squad.
"Tonight wasn't the prettiest but we got the job done and we got that little bit of luck at the end. I think we have merited that over the season."
McCall added: "We have taken it to the last game, we are proud to be in Europe and the only downside is wee Craig Moore looks like he has tweaked his cartilage and will probably need that out."
Inverness manager John Hughes felt his side deserved at least a point - and a penalty for a handball when Fraser Kerr blocked a cross.
Hughes said: "The full-back stopped a cross like a goalkeeper, so for me that's a penalty. But we put enough into it, dominated the whole second half, had them right on the back foot, played with a little more hunger and desire. Everything I'm looking for from an Inverness team. We played with more purpose and pace in the second half.
"I felt we were the better team, especially in the second half, but goals win games and if we keep conceding like that, we'll not win many."