Kevin O'Connor's injury-time penalty cancelled out Massimo Luongo's 70th- minute opener for the Robins - his thumping finish with 90 seconds to go setting the tie up perfectly for the second leg at Griffin Park on Monday.
It was rough luck for Tottenham loanee Luongo, who went from hero to villain as he made the crucial foul at the end of Brentford's best move of the night.
MacDonald said: "The timing of the goal is obviously disappointing but it is 1-1 and we are both in the tie.
"I thought the conditions were difficult for both teams. No team really handled it in the way they'd have liked to.
"I think both teams were nervous as well as it was a big game. At half-time we felt we could do better as there wasn't really enough chances.
"I didn't think we passed it as much as we usually do, we got ourselves in good positions but didn't make enough good chances.
"The timing of the goal is tough to a certain extent and they are disappointed in there but we are evenly matched, it is a one-off game and it will be about who recovers quickest."