Sent into bat, the visitors reached 78 for two at lunch at the KSCA Stadium.
Guyanese batsmen Leon Johson and Narasingh Deonaraine were batting on 34 and 10, respectively, after West Indies A lost the two openers Brathwaite (1) and Kieran Powell (21).
Zaheer, who had a dismal outing in the Shimoga Test with figures of two for 93, somewhat found his rhythm and steamed in as the two openers played cautiously against the left-arm pacer.
The pace spearhead had the last laugh against the right-handed Barbadian when he forced him to play an away-going delivery into the hands of wicketkeeper Uday Kaul.
India A captain Cheteshwar Pujara was happy to see the back of Brathwaite, who had been a thorn in the flesh for the host bowlers, posting two half centuries and a century in the series so far.
After the fall of Brathwaite, Johnson walked in to join Powell and both put on a 45-run partnership for the second wicket before Dhawal Kulkarni, who got his first chance to play in the series, bowled the opener.