Mihajlovic's men were on track to take third place from Rafael Benitez's side after Eder's fine finish prior to the hour-mark, and the dismissal of Napoli defender Kalidou Koulibaly with six minutes of regulation remaining.
But a Daniel Zapata header in injury time saw the sides split the points, and Napoli hold onto their position in the UEFA Champions League spots.
Sampdoria boss Mihajlovic rued their late lapse, but did not blame his players for failing to get all three points against "big club" Napoli.
"Considering we dominated the match, I think drawing like this hurts everyone," Mihajlovic told Sky Sport Italia.
"We deserved the victory for our performance, but this is football and against a big club you get punished at the first distraction.
"Having played against Napoli, who in recent years have always been in the top two or three teams in Italy and had more shots on target than anyone else this season, we allowed them hardly any chances. I think we can only be proud of that.
"Napoli threw everything they had at us, four strikers and the goal was probably our first mistake as [Djamel] Mesbah didn't follow Zapata.
"I cannot reproach my lads for anything, as they gave their all. They gave their all."
Mihajlovic defended his 79th-minute substitution of midfielder Luca Rizzo, who was replaced by Manolo Gabbiadini - a striker.
"I saw Rizzo was tired and Napoli were putting us under pressure on the wings, so I introduced a striker to put more pressure on their full-backs and keep them from crossing," Mihajlovic added.
"Unfortunately, they did score with a cross from that side, but we were forced into two substitutions with [Pedro] Obiang and [Roberto] Soriano injured, so we had to adapt our original plans.
"If we'd been able to make the substitutions we had planned, then perhaps we would've won rather than drawn this game."