Mendis played a key role in his team's eight-wicket win over India in the first one-dayer of the five-match series here, finishing with 3-21 off nine overs to restrict the tourists to 146.
Sri Lanka achieved the modest target with more than 15 overs to spare, with the man-of-the-match award going to Mendis.
"It's difficult to pick him (Mendis). He is a very different bowler. Even if you pick him, by the time you realise what ball it is, it gets really late to play a big shot," said Dhoni.
"In one-day cricket, it is not only about playing him but also rotating the strike because you don't want a bowler to end up with 10 overs for 20 runs. We need to find a way to rotate the strike.
"I have not seen any bowler like him. He is an unusual bowler. The only option right now is to play more and more of him and that's the only way of getting better."
The Indian captain said losing early wickets affected his team's chances of posting a decent total.
"We misread the wicket a bit. There was a fair bit in the pitch for bowlers early in the match. The Sri Lankans bowled really well as they got early wickets. Credit goes to them," said Dhoni, who had elected to bat first.
"Later on, Mendis put the pressure. The only thing we were doing was to catch up and it gets really tough in one-day games if you lose too many wickets up front."