The Japanese international was heavily linked with a move away from Bologna all summer and Tottenham were the club who initially pushed to sign him earlier in the window.
But the track leading to Tottenham faded with each passing week and eventually, Arsenal forced the issue on deadline day and signed the defender for a fee worth more than €22m.
Mihajlovic conceded that selling the Japanese international was always part of the plans at Bologna for the summer.
But admitted that this departure still hurts a bit as the defender eventually left with just hours left in the transfer window.
Asked if he was happy with Bologna’s transfer window, the coach told Italian outlet Tutto Mercato: “Until yesterday, yes but today, a little less.
“Tomiyasu’s sale was planned but leaving just five to six hours before the end of the transfer window, gnaws at you a bit.”
Tomiyasu can play both right-back and centre-back and was on Arsenal’s radar throughout the transfer window despite the last-minute nature of the deal.